@article {pmid40736903,
year = {2025},
author = {Papastolopoulou, C and Yang, Z and van Workum, DM and Wijfjes, RY and Smit, S},
title = {High-Quality Plant Genomes for and through Pangenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {293-316},
doi = {10.1007/978-1-0716-4702-8_14},
pmid = {40736903},
issn = {1940-6029},
mesh = {*Genome, Plant ; *Genomics/methods ; Molecular Sequence Annotation ; *Plants/genetics ; Genetic Variation ; Capsicum/genetics ; },
abstract = {The field of comparative genomics is shifting toward pangenomics, aiming to alleviate the reference bias observed in reference-based approaches. High-quality genomes are needed as input for pangenomics, as explained by the principle of "garbage in, garbage out". Errors in an assembly or annotation will lead to technical variation in a pangenome, while it is meant to reveal genuine biological variation only. Achieving the required assembly and annotation quality remains challenging, particularly in plants, given the complexity in genome size, ploidy level, and repeat content present in the plant kingdom.Nevertheless, the (technical) variation uncovered by pangenomics can, in turn, guide iterative refinements that yield high-quality genomes. The comparative approach is especially powerful to identify "abnormalities" in a set of genomes, which cannot be detected from traditional, stand-alone quality assessment. Two use cases, on roses and chili peppers, illustrate the role of pangenomics in this iterative process leading toward meaningful pangenome analyses. Thus, we argue that high-quality genomes can be achieved through pangenomics, facilitating the convergence on real genetic variation underlying complex traits and diseases, not only in plants but also in other organisms.},
}

*Genome, Plant
*Genomics/methods
Molecular Sequence Annotation
*Plants/genetics
Genetic Variation
Capsicum/genetics

@article {pmid40736902,
year = {2025},
author = {Gifford, H and Wilson, D and Rhodes, J and Farrer, RA},
title = {Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {263-291},
pmid = {40736902},
issn = {1940-6029},
mesh = {Humans ; *Candidiasis/microbiology/diagnosis ; *Candida auris/genetics/pathogenicity ; Animals ; Computational Biology/methods ; Host-Pathogen Interactions ; *Candida/genetics ; },
abstract = {Discovery science in Medical Mycology requires a range of tools, from optimized experimental models to near-patient clinical applications, with the common goal of reducing morbidity and mortality from fungal diseases. Assembly tools underpin bioinformatic discovery across this spectrum of research, setting the scene for genomic enquiry, and promising an unprecedented wave of breakthrough in mechanistic understanding of pathobiology that could unearth critical diagnostic and treatment advances. This chapter examines the investigation of Candida auris, an emerging human fungal pathogen, in the context of clinic detection and treatment of infection. In the laboratory, we cover the use of the Arabian Killifish (AK) as a non-model organism to understand transcriptional responses to both host and pathogen during infection.},
}

Humans
*Candidiasis/microbiology/diagnosis
*Candida auris/genetics/pathogenicity
Animals
Computational Biology/methods
Host-Pathogen Interactions
*Candida/genetics

@article {pmid40732189,
year = {2025},
author = {Mashzhan, A and Smekenov, I and Bakiyev, S and Utegenova, K and Samatkyzy, D and Daniyarov, A and Kairov, U and Sarbassov, D and Bissenbaev, A},
title = {Whole-Genome Sequencing of a Potentially Novel Aeromonas Species Isolated from Diseased Siberian Sturgeon (Acipenser baerii) Using Oxford Nanopore Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071680},
pmid = {40732189},
issn = {2076-2607},
support = {АP23487566//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakh-stan/ ; },
abstract = {Aeromonas spp. are opportunistic pathogens that are widely distributed in water sources, with several species being associated with fish and human diseases. We have previously identified an Aeromonas AB005 isolate from diseased Acipencer baerii. This isolate was identified as A. hydrophila based on the 16S rRNA and gyrB gene sequences. However, this novel strain does not produce indole and tested negative for ornithine decarboxylase and d-xylose fermentation-differences that set it apart from typical A. hydrophila strains. In the present study, this strain was subjected to whole-genome sequencing and compared with the genomes of the type strain (Aeromonas hydrophila ATCC 7966[T]) and other Aeromonas spp. Comprehensive genome analysis suggests that AB005 represents a distinct species within the genus. The draft genome of the AB005 strain comprises 4,780,815 base pairs with a GC content of 61.2% and contains 6104 predicted protein-coding sequences along with numerous genes implicated in antibiotic resistance. The core/pan-genome analysis reveals extensive genetic diversity, indicative of a dynamic genomic structure. These findings collectively underscore the taxonomic distinction of the AB005 strain as a novel species and highlight its potential pathogenic implications in aquaculture and public health settings.},
}

@article {pmid40729388,
year = {2025},
author = {Riaz, MR and Sosa Marquez, I and Lindgren, H and Levin, G and Doyle, R and Romero, MC and Paoli, JC and Drnevich, J and Fields, CJ and Geddes, BA and Marshall-Colón, A and Heath, KD},
title = {Mobile gene clusters and coexpressed plant-rhizobium pathways drive partner quality variation in symbiosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {31},
pages = {e2411831122},
doi = {10.1073/pnas.2411831122},
pmid = {40729388},
issn = {1091-6490},
support = {IOS-1645875//NSF (NSF)/ ; DBI-2022049//NSF (NSF)/ ; IOS-2243821//NSF (NSF)/ ; na//Consejo Nacional de Humanidades, Ciencias y Tecnologías (Conahcyt)/ ; na//UofI | UIUC | Carl R. Woese Institute for Genomic Biology (IGB)/ ; IOS- 2243818//NSF (NSF)/ ; },
mesh = {*Symbiosis/genetics ; *Sinorhizobium meliloti/genetics ; *Multigene Family ; Root Nodules, Plant/microbiology/genetics ; Genetic Variation ; Transcriptome ; *Rhizobium/genetics ; Gene Regulatory Networks ; },
abstract = {Plant-microbe symbioses such as the legume-rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence-absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.},
}

*Symbiosis/genetics
*Sinorhizobium meliloti/genetics
*Multigene Family
Root Nodules, Plant/microbiology/genetics
Genetic Variation
Transcriptome
*Rhizobium/genetics
Gene Regulatory Networks

@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}

@article {pmid40728297,
year = {2025},
author = {Guo, X and He, Z-G},
title = {Pangenome-scale annotation of mycobacteriophages for dissecting phage-host interactions based on a sequence clustering and structural homology analysis strategy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050825},
doi = {10.1128/msystems.00508-25},
pmid = {40728297},
issn = {2379-5077},
abstract = {With the increasing severity of bacterial drug resistance, there is a growing need for phages with well-defined genetic backgrounds to combat drug-resistant infections. Mycobacteriophages constitute the largest genome-sequenced phage group; however, the vast majority of these phage proteins have not yet been effectively annotated. In this study, we employed a structure-based similarity search approach to improve protein annotation. Through the application of this approach to 240,754 proteins from 2,169 mycobacteriophage genomes, we increased the protein annotation rate from 34% to 52.11%. Additionally, we identified a series of predicted counter-defense proteins, including anti-CRISPR proteins and antitoxins, and inferred the potential interaction network of phage-encoded proteins involved in replication, transcription, and translation with host-associated molecular machinery. This study addresses a substantial gap in the current knowledge of the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.IMPORTANCEMycobacteriophages constitute the largest group of phages with sequenced genomes. However, a significant portion of these phage proteins have not yet been effectively annotated, seriously hindering our understanding of the basic biological processes of phage-host interactions and their practical applications. This study utilized a structure-based similarity search approach to enhance phage protein annotation. This approach led to the identification of novel predicted protein folds, structural domain fusion phenomena, and putative new enzymes. Additionally, the study identified a series of phage-encoded proteins that may play a role in hijacking host-associated replication, transcription, and translation processes, providing insights into the molecular mechanisms underlying mycobacteriophage interactions with host machinery. This study addresses a critical knowledge gap regarding the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.},
}

@article {pmid40726548,
year = {2025},
author = {Li, Q and Fu, Y and Zhang, C and Zhang, G and Zhao, Y and Wang, Y and Dou, Y and Gao, L and Abdullah, S and Ma, X and Su, Y and Song, X},
title = {Deciphering the near-complete genome and conducting pan-genome analysis of Brassica oleracea.},
journal = {Horticulture research},
volume = {12},
number = {8},
pages = {uhaf189},
pmid = {40726548},
issn = {2662-6810},
}

@article {pmid40724005,
year = {2025},
author = {Tristancho-Baró, A and López-Calleja, AI and Milagro, A and Ariza, M and Viñeta, V and Fortuño, B and López, C and Latorre-Millán, M and Clusa, L and Badenas-Alzugaray, D and Martínez, R and Torres, C and Rezusta, A},
title = {Mechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/antibiotics14070703},
pmid = {40724005},
issn = {2079-6382},
abstract = {Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was blaNDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512. Genes associated with toxin-antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems-especially in those encoded by fec, fhu, and cir operons-play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies.},
}

@article {pmid40722552,
year = {2025},
author = {Moustakli, E and Christopoulos, P and Potiris, A and Zikopoulos, A and Mavrogianni, D and Karampas, G and Kathopoulis, N and Anagnostaki, I and Domali, E and Tzallas, AT and Drakakis, P and Stavros, S},
title = {Long-Read Sequencing and Structural Variant Detection: Unlocking the Hidden Genome in Rare Genetic Disorders.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/diagnostics15141803},
pmid = {40722552},
issn = {2075-4418},
abstract = {Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption.},
}

@article {pmid40721945,
year = {2025},
author = {Zhang, X and Chen, X and Wu, X and Liu, Y and Wei, Y},
title = {Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27420},
pmid = {40721945},
issn = {2045-2322},
support = {42073077//the National Natural Science Foundation of China/ ; },
abstract = {In this study, we aimed to clarify the taxonomic positions of Micromonospora veneta DSM 109713[T] and Micromonospora coerulea JCM 3175[T] using whole-genome phylogenetic analysis, pangenomic analysis and chemotaxonomic characteristics. The 16S rRNA gene sequences of veneta DSM 109713[T] and M. coerulea JCM 3175[T] were highly similar (99.2%), and in the phylogenetic trees constructed using whole genome sequences and 16S rRNA gene sequences, M. veneta DSM 109713[T] and M. coerulea JCM 3175[T] clustered together and formed a clade. The values of average amino acid (AAI), ANI-BLAST (ANIb) and ANI-MUMmer (ANIm), and digital DNA-DNA hybridization (dDDH) between M. veneta DSM 109713[T] and M. coerulea JCM 3175[T] were 97.57%, 97.81%, 98.40%, 85.0%, respectively, which are all greater than the thresholds used for species delimitation (AAI: 95.5%, ANI: 95-96%, and dDDH: 70%). Most phenotypic and chemotaxonomic features between the two species were similar, with only a few differences. Based on the combined evidence from genomic and phenotypic comparison, we propose Micromonospora veneta as a later heterotypic synonym of Micromonospora coerulea.},
}

@article {pmid40721805,
year = {2025},
author = {Wen, H and Yang, J and Zhao, X and Wang, X and Lei, J and Li, Y and Du, W and Li, D and Xu, Y and Lonardi, S and Pan, W},
title = {TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {227},
doi = {10.1186/s13059-025-03685-5},
pmid = {40721805},
issn = {1474-760X},
support = {32100501//National Natural Science Foundation of China/ ; ZDRW202503//the Agricultural Science and Technology Innovation Program/ ; Y2025QC36//the Youth Innovation Program of the Chinese Academy of Agricultural Sciences/ ; CAAS-CSIAF-202301//The Agricultural Science and Technology Innovation Program/ ; },
mesh = {Humans ; *Tandem Repeat Sequences ; *Algorithms ; Solanum lycopersicum/genetics ; Centromere/genetics ; *Sequence Analysis, DNA/methods ; Software ; Telomere/genetics ; },
abstract = {The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.},
}

Humans
*Tandem Repeat Sequences
*Algorithms
Solanum lycopersicum/genetics
Centromere/genetics
*Sequence Analysis, DNA/methods
Software
Telomere/genetics

@article {pmid40721218,
year = {2025},
author = {Hu, M and Wan, P and Chen, C and Tang, S and Chen, J and Wang, L and Chakraborty, M and Zhou, Y and Chen, J and Gaut, BS and Emerson, JJ and Liao, Y},
title = {Accurate, scalable structural variant genotyping in complex genomes at population scales.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf180},
pmid = {40721218},
issn = {1537-1719},
abstract = {Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce SVGAP, a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pan-genome construction and facilitates the interpretation of previously unexplored genomic regions.},
}

@article {pmid40716970,
year = {2025},
author = {Rodriguez-Valera, F and Molina-Pardines, C},
title = {On the biological meaning of the population pangenome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.07.004},
pmid = {40716970},
issn = {1878-4380},
abstract = {The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool within a single population, defined as cells of the same species coexisting in the same time and place. This single-population pangenome reflects the minimal flexible gene repertoire required in a specific environmental context. Recent long-read metagenomic studies of marine prokaryotes show that local population pangenomes remain large, often comprising thousands of genes. Specifically, cells belonging to the same species of the streamlined alfaproteobacterium Pelagibacter, coming from the same sampling site and even sample, contain more than a thousand genes. Many of these genes are related variants that collectively expand the population's metabolic potential, akin to paralogs within a single large genome. We propose for them the name 'metaparalogs' together with the idea that these data reflect cooperative, population-level strategies, where the flexible genome operates as a public good (sensu Samuelson), enhancing both adaptability and ecological resilience. A role for extracellular vesicles in facilitating resource sharing is also suggested.},
}

@article {pmid40719802,
year = {2025},
author = {Ajdig, M and Mbarki, A and Chouati, T and Rached, B and Gardoul, M and Filali-Maltouf, A and Talbi, C and Fahime, EE and Melloul, M},
title = {Comprehensive genomic and pan-genomic analysis of the drought-tolerant Bacillus halotolerans strain OM-41 isolated from Olive rhizosphere, reveals potential plant growth-promoting and biocontrol traits.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {276},
pmid = {40719802},
issn = {1573-0972},
mesh = {*Rhizosphere ; Phylogeny ; Droughts ; *Olea/microbiology/growth & development ; *Bacillus/genetics/isolation & purification/classification/physiology ; Genome, Bacterial ; Genomics ; Soil Microbiology ; Indoleacetic Acids/metabolism ; Stress, Physiological ; Biological Control Agents ; Plant Development ; Whole Genome Sequencing ; Siderophores/metabolism ; Plant Growth Regulators/metabolism ; },
abstract = {Abiotic and biotic stresses increasingly threaten plant health and productivity, causing substantial yield losses in vital crops. In this study, 99 rhizobacteria isolated from Moroccan olive rhizospheres, OM-41 was selected as the most potent strain, exhibiting exceptional drought tolerance (thriving at Aw 0.859), thermotolerance (up to 55 °C), and halotolerance (15% NaCl), alongside plant growth-promoting (PGP) traits such as phosphate solubilization, indole-acetic acid (IAA), gibberellic acid, siderophore production, and hydrolytic enzyme secretion. The strain suppressed V. dahliae via diffusible and volatile antifungal compounds, achieving 76% and 69% inhibition rates, respectively. Whole-genome sequencing revealed a 4.2 Mbp genome (43.5% GC content) with 4362 protein-coding genes. Phylogenetic analyses confirmed its classification as B. halotolerans. Genomic annotation identified 11 secondary metabolite clusters and stress-related genes, including those linked to phosphate solubilization (phy, pho, pst family), IAA synthesis (dhaS, trp operon), siderophores (dhb cluster), nitrogen fixation (nif, suf, urt genes), ammonia production (gudB, nasD/E), biofilm formation (tasA, bsl genes), antifungal volatiles (alsD, ilv operon), hydrolytic enzymes (e.g., amyE, eglS), and vitamin biosynthesis (thiamine/riboflavin operons). Pangenome analysis of 79 B. halotolerans strains highlighted an open pangenome with 12,679 total genes (2270 core, 2382 accessory and 8027 unique); OM-41 harbored 98 unique genes. These findings underscore potential of OM-41 as a biofertilizer and biocontrol agent, leveraging antibiosis, resource competition, and plant defense induction to mitigate pathogens and abiotic stresses. Up to our knowledge, this is the first work that evaluates the pangenome features of B. halotolerans, offering insights into its genomic plasticity and adaptive traits. The strain's multifunctional PGP capabilities and stress resilience position it as a promising solution for sustainable agriculture in challenging environments.},
}

*Rhizosphere
Phylogeny
Droughts
*Olea/microbiology/growth & development
*Bacillus/genetics/isolation & purification/classification/physiology
Genome, Bacterial
Genomics
Soil Microbiology
Indoleacetic Acids/metabolism
Stress, Physiological
Biological Control Agents
Plant Development
Whole Genome Sequencing
Siderophores/metabolism
Plant Growth Regulators/metabolism

@article {pmid40709915,
year = {2025},
author = {Qin, C and Lypaczewski, P and Sayeed, MA and Cuénod, A and Brinkley, L and Creasy-Marrazzo, A and Cato, ET and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, Y and Kamat, MN and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Vibrio cholerae lineage and pangenome diversity vary geographically across Bangladesh over 1 year.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001437},
pmid = {40709915},
issn = {2057-5858},
mesh = {Bangladesh/epidemiology ; *Vibrio cholerae/genetics/classification/drug effects/isolation & purification ; *Cholera/epidemiology/microbiology ; Humans ; *Genome, Bacterial ; Phylogeny ; Genetic Variation ; Disease Outbreaks ; Whole Genome Sequencing ; },
abstract = {Cholera is an acute diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in V. cholerae isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018-2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the V. cholerae pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.},
}

Bangladesh/epidemiology
*Vibrio cholerae/genetics/classification/drug effects/isolation & purification
*Cholera/epidemiology/microbiology
Humans
*Genome, Bacterial
Phylogeny
Genetic Variation
Disease Outbreaks
Whole Genome Sequencing

@article {pmid40707445,
year = {2025},
author = {Nassir, N and Almarri, MA and Kumail, M and Mohamed, N and Balan, B and Hanif, S and AlObathani, M and Jamalalail, B and Elsokary, H and Kondaramage, D and Shiyas, S and Kosaji, N and Satsangi, D and Abdelmotagali, MHS and Abou Tayoun, A and Ahmed, OZS and Youssef, DF and Suwaidi, HA and Albanna, A and S Du Plessis, S and Khansaheb, HH and Alsheikh-Ali, A and Uddin, M},
title = {A draft UAE-based Arab pangenome reference.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6747},
pmid = {40707445},
issn = {2041-1723},
mesh = {Humans ; United Arab Emirates ; *Arabs/genetics ; *Genome, Human/genetics ; Genetic Variation ; Haplotypes ; Genetics, Population ; Gene Duplication ; },
abstract = {Pangenomes provide a robust and comprehensive portrayal of genetic diversity in humans, but Arab populations remain underrepresented. We present a preliminary UAE-based Arab Pangenome Reference (UPR) utilizing 53 individuals of diverse Arab ethnicities residing in the United Arab Emirates. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads. This approach yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of previously uncharacterized euchromatic sequences absent from existing human pangenomes, the T2T-CHM13 and GRCh38 reference human genomes, and other public datasets. Moreover, we identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome, not present in linear and pangenome references and public datasets. We detected 883 gene duplications, including the TATA-binding protein gene TAF11L5, which was uniquely duplicated across all Arab populations and that included 15.06% of genes associated with recessive diseases. By exploring the mitochondrial pangenome, we identified 1,436 bp of previously unreported sequences. Our study provides a valuable resource for future genetic research and genomic medicine initiatives in Arab population and other population with similar genetic backgrounds.},
}

Humans
United Arab Emirates
*Arabs/genetics
*Genome, Human/genetics
Genetic Variation
Haplotypes
Genetics, Population
Gene Duplication

@article {pmid40704999,
year = {2025},
author = {Ono, M and Yamaguchi, M and Motooka, D and Hirose, Y and Higashi, K and Sumitomo, T and Miyoshi-Akiyama, T and Okuno, R and Yamaguchi, T and Kawahara, R and Otsuka, H and Nakanishi, N and Kazawa, Y and Nakagawa, C and Yamaguchi, R and Sakai, H and Matsumoto, Y and Ikebe, T and Kawabata, S},
title = {Identifying genetic variations in emm89 Streptococcus pyogenes associated with severe invasive infections.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40704999},
issn = {2050-084X},
support = {20KK0210//Japan Society for the Promotion of Science/ ; 22H03262//Japan Society for the Promotion of Science/ ; 22K19618//Japan Society for the Promotion of Science/ ; 22K19619//Japan Society for the Promotion of Science/ ; 23H03073//Japan Society for the Promotion of Science/ ; 23K19687//Japan Society for the Promotion of Science/ ; 24K19854//Japan Society for the Promotion of Science/ ; 2022B05//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; 2025B01//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; 2025B13//Joint Research Program of the Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University/ ; JPMJSP2138//Japan Science and Technology Agency SPRING/ ; JP17fk0108044//AMED/ ; JP20fk0108130//AMED/ ; JP20wm0325001//AMED/ ; JP243fa727001h//AMED/ ; EX22701//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh230035//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh240003//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; jh250016//Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN)/ ; },
mesh = {*Streptococcus pyogenes/genetics/pathogenicity ; Humans ; *Streptococcal Infections/microbiology/pathology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Genetic Variation ; Virulence/genetics ; INDEL Mutation ; },
abstract = {Streptococcus pyogenes causes mild human infections as well as life-threatening invasive diseases. Since the mutations known to enhance virulence to date account for only half of the severe invasive infections, additional mechanisms/mutations need to be identified. Here, we conducted a genome-wide association study of emm89 S. pyogenes strains to comprehensively identify pathology-related bacterial genetic factors (single-nucleotide polymorphisms [SNPs], indels, genes, or k-mers). Japanese (n = 311) and global (n = 666) cohort studies of strains isolated from invasive or non-invasive infections revealed 17 and 1075 SNPs/indels and 2 and 169 genes, respectively, that displayed associations with invasiveness. We validated one of them, a non-invasiveness-related point mutation, fhuB T218C, by structure predictions and introducing it into a severe invasive strain and confirmed that the mutant showed slower growth in human blood. Thus, we report novel mechanisms that convert emm89 S. pyogenes to an invasive phenotype and a platform for establishing novel treatments and prevention strategies.},
}

*Streptococcus pyogenes/genetics/pathogenicity
Humans
*Streptococcal Infections/microbiology/pathology
Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Genetic Variation
Virulence/genetics
INDEL Mutation

@article {pmid40704797,
year = {2025},
author = {Yu, Z and Wang, R},
title = {Genomic-enabled classification of three Mycobacteroides abscessus subspecies and an effective subspecies-specific identification method.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0069725},
doi = {10.1128/jcm.00697-25},
pmid = {40704797},
issn = {1098-660X},
abstract = {Mycobacteroides abscessus (Mab) is a clinically significant non-tuberculous mycobacterium. It comprises three distinct subspecies being considered to have different macrolide susceptibilities, transmission patterns, and treatment outcomes. In this study, systematic analysis was conducted on 2,006 Mab genomes deposited in the National Center for Biotechnology Information genome database, and the taxonomic classification of their subspecies was revised accordingly. The findings revealed that: (i) in terms of three distinct subspecies classification, the analysis based on core genes and average nucleotide identity (ANI) values was completely consistent; (ii) ANI was a reliable criterion for Mab species and subspecies classification, with defined thresholds of 95% ANI for species-level and 98% ANI for subspecies-level differentiations; and (iii) the integrity of the erm(41) gene or the similarity of the rpoB gene was an unreliable characteristic for Mab subspecies, and the assertions that subspecies massiliense lack inducible resistance to macrolides also cannot be sustained. Moreover, through a subspecies re-classification of genomes and pangenome analysis, Mab subspecies-specific genes were successfully identified, and a novel single-gene test with enhanced clinical applicability was developed. Additionally, the impact of reference genome selection on taxonomic classification highlighted the importance of adopting a standardized set of reference genomes in species/subspecies identification to significantly enhance the comparability across different studies.IMPORTANCEMycobacteroides abscessus (Mab) is a clinically challenging non-tuberculous mycobacteria species. The accurate identification of subspecies is of utmost importance for clinical diagnosis and treatment, as well as for research on pathogenicity, drug resistance, and other related aspects. This study provided a clear average nucleotide identity threshold for Mab subspecies classification, as well as revised options of the three Mab subspecies, new and accurate Mab subspecies-special biomarker, and a detection technique with practical clinical application.},
}

@article {pmid40703244,
year = {2025},
author = {Chen, S and Agah, G and Blom, J and Walker, ED},
title = {Molecular characterization, comparative genome analysis and resistance determinants of three clinical Elizabethkingia miricola strains isolated from Michigan.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582121},
pmid = {40703244},
issn = {1664-302X},
abstract = {INTRODUCTION: Elizabethkingia miricola is a gram-negative bacterium that causes life-threatening infections in vulnerable populations. Unlike other species in the Elizabethkingia genus, E. miricola also leads to meningitis-like diseases in aquatic invertebrates such as frogs, raising concerns about its zoonotic transmission potential. Management of its infection is complicated by unclear transmission pathways and multi-drug resistance.

METHODS: In this study, we analyzed three clinical strains (E. miricola Mich-1, Mich-2, and Mich-3) isolated from patients in Michigan using morphology observations, biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF/MS), and genome sequencing.

RESULTS: Average Nucleotide Identity (ANI) analysis revealed that the Michigan strains were nearly identical and shared 96.52% identity with the type strain E. miricola DSM 14571, confirming their classification as E. miricola. Comprehensive comparative genomic analyses were conducted across 28 strains, including human isolates and strains from invertebrates like frogs. The strains exhibited open pan-genome characteristics. Mich-1 shared 3,199 genes (83.2%) with human isolates but fewer genes with frog-derived isolates (ranging from 3,319 to 3,375). This phylogenetic analysis highlights regional variation and the global diversity of E. miricola isolates, revealing connections between clinical and environmental strains. Antibiotic susceptibility testing revealed that the three clinical strains were resistant to 13 out of 16 tested drugs, with susceptibility only to trimethoprim/sulfamethoxazole and ciprofloxacin. The strains carried five β-lactamase-encoding genes (BlaB-10, BlaB-39, CME-1, CME-2, and GOB-25), conferring resistance to penams, cephalosporins, and carbapenems. Several virulence-associated genes were conserved across clinical and frog isolates. These genes contribute to stress adaptation, adherence, and immune modulation.

DISCUSSION: This study underscores the evolutionary adaptability of E. miricola genomes, highlighting their capacity to acquire genetic traits that enable survival in diverse niches. This adaptability facilitates the emergence of more resistant and virulent strains, posing significant threats to both human and animal health.},
}

@article {pmid40702183,
year = {2025},
author = {Logsdon, GA and Ebert, P and Audano, PA and Loftus, M and Porubsky, D and Ebler, J and Yilmaz, F and Hallast, P and Prodanov, T and Yoo, D and Paisie, CA and Harvey, WT and Zhao, X and Martino, GV and Henglin, M and Munson, KM and Rabbani, K and Chin, CS and Gu, B and Ashraf, H and Scholz, S and Austine-Orimoloye, O and Balachandran, P and Bonder, MJ and Cheng, H and Chong, Z and Crabtree, J and Gerstein, M and Guethlein, LA and Hasenfeld, P and Hickey, G and Hoekzema, K and Hunt, SE and Jensen, M and Jiang, Y and Koren, S and Kwon, Y and Li, C and Li, H and Li, J and Norman, PJ and Oshima, KK and Paten, B and Phillippy, AM and Pollock, NR and Rausch, T and Rautiainen, M and Song, Y and Söylev, A and Sulovari, A and Surapaneni, L and Tsapalou, V and Zhou, W and Zhou, Y and Zhu, Q and Zody, MC and Mills, RE and Devine, SE and Shi, X and Talkowski, ME and Chaisson, MJP and Dilthey, AT and Konkel, MK and Korbel, JO and Lee, C and Beck, CR and Eichler, EE and Marschall, T},
title = {Complex genetic variation in nearly complete human genomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40702183},
issn = {1476-4687},
abstract = {Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps[1,2] and reaching telomere-to-telomere status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8 and AMY1/AMY2, and fully resolve 1,852 complex structural variants. In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite higher-order repeat array length and characterize the pattern of mobile element insertions into α-satellite higher-order repeat arrays. Although most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference[1] significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference[3] to a median quality value of 45. Using this approach, 26,115 structural variants per individual are detected, substantially increasing the number of structural variants now amenable to downstream disease association studies.},
}

@article {pmid40697987,
year = {2025},
author = {Boondech, A and Ainmani, P and Khieokhajonkhet, A and Boonsrangsom, T and Pongcharoen, P and Rungrat, T and Sujipuli, K and Ratanasut, K and Aeksiri, N},
title = {Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697987},
issn = {2516-8290},
abstract = {Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.},
}

@article {pmid40697354,
year = {2025},
author = {Hölzer, M and Reuschel, C and Vorimore, F and Laroucau, K and Sachse, K},
title = {Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs.},
journal = {Access microbiology},
volume = {7},
number = {2},
pages = {},
pmid = {40697354},
issn = {2516-8290},
abstract = {Recently discovered obligate intracellular bacteria belonging to the genus Chlamydiifrater with the species of Chlamydiifrater phoenicopteri and Chlamydiifrater volucris were studied to explore the composition of their genomes and their relatedness to Chlamydia, the other genus of the family Chlamydiaceae. We investigated 4 isolates of Cf. volucris, 2 of them newly sequenced, and one of Cf. phoenicopteri alongside 12 representatives of the Chlamydia species. Our study uncovers previously unrecognized genomic structures within Chlamydiifrater using a hybrid sequencing approach and advanced annotation pipelines, providing insights into species-specific adaptations and evolutionary dynamics. The integration of long-read sequencing data, comprehensive re-annotation strategies and pan-genomics enabled the localization of the unique plasticity zone and the identification of novel gene clusters in Chlamydiifrater strains, which improves our understanding of chlamydial genome architecture and plasticity in the family Chlamydiaceae. Our analysis revealed that 761 CDS (~80%) are shared among members of both genera. We further identified 158 unique genes of Chlamydiifrater species, but their annotation remains challenging because of the absence of functionally annotated orthologs in public databases. A full-length ompA gene encoding the major outer membrane porin was seen in all Chlamydiifrater strains. We also describe the localization and structure of multiple truncated CDS of ompA family members, representing one of this study's most interesting findings. While genome analysis of Chlamydiifrater spp. confirmed numerous common features shared with representatives of the genus Chlamydia, many unique genomic elements were identified that underpin the distinct phenotype and separate genetic position of these new microorganisms.},
}

@article {pmid40696396,
year = {2025},
author = {Chen, Y and Bao, R and Li, N and Fang, T and Yin, X and Qin, L and Hu, B and Miao, Q},
title = {Whole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {44},
pmid = {40696396},
issn = {1476-0711},
support = {2024ZSFZ39//Zhongshan Hospital/ ; 2024J08352//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification ; Humans ; Anti-Bacterial Agents/pharmacology ; *Genome, Bacterial ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Phenotype ; *Recombination, Genetic ; Macrolides/pharmacology ; Genetic Variation ; Mycobacterium Infections, Nontuberculous/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.

METHODS: We performed whole-genome sequencing and phenotypic antimicrobial susceptibility testing on 109 Mab isolates collected at zhongshan hospital from 2018 to 2023.

RESULTS: The results indicate that recombination, especially distributed conjugation transfer, promotes the formation and sustained diversity of Mab subspecies. Through pangenome analysis, the synergistic gain/loss of accessory genes was found to contribute to different metabolic profiles and the ability to adapt to oxidative stress, facilitating strain adaptation to host environments. We conducted phenotypic antimicrobial susceptibility testing, revealing resistance to macrolide antibiotics differed among subspecies. We identified 24 genes whose gain or loss may increase the likelihood of macrolide resistance, including those involved in biofilm formation, the stress response, virulence, biotin synthesis, and fatty acid metabolism. Genomic variations within Mab species may have significant implications for disease epidemiology, infection pathogenesis, and host interactions.

CONCLUSIONS: Our findings provide a valuable genetic basis for the success of Mab as a highly adaptive and drug-resistant pathogen, informing current efforts to control and treat Mab infections, including strategies targeting specific sequence types or lineages.},
}

*Mycobacterium abscessus/genetics/drug effects/classification/isolation & purification
Humans
Anti-Bacterial Agents/pharmacology
*Genome, Bacterial
Whole Genome Sequencing
Microbial Sensitivity Tests
Phenotype
*Recombination, Genetic
Macrolides/pharmacology
Genetic Variation
Mycobacterium Infections, Nontuberculous/microbiology
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid40695073,
year = {2025},
author = {Hinthong, W and Phelan, J and Hussain, A and Mazumder, R and Azra, and Haq, IU and Ullah, I and Roberts, T and Thawong, N and Billows, N and Campino, S and Khan, TA and Mondal, D and Clark, TG},
title = {Genomic insights into Klebsiella pneumoniae: Virulence, resistance, and transmission in South and Southeast Asia.},
journal = {International journal of medical microbiology : IJMM},
volume = {320},
number = {},
pages = {151666},
doi = {10.1016/j.ijmm.2025.151666},
pmid = {40695073},
issn = {1618-0607},
abstract = {BACKGROUND: Klebsiella pneumoniae has long posed a significant challenge in clinical settings worldwide, particularly due to its carbapenemase production and multidrug-resistant (MDR) characteristics. While extensive genomic studies of K. pneumoniae have been conducted globally, research in Asia, particularly South Asia, remains limited.

OBJECTIVES: This study aims to address and compare the genomic characteristics of K. pneumoniae isolates from South Asia and Southeast Asia, including virulence, antimicrobial resistance (AMR), plasmids, and mobile genetic elements (MGE) profiles, as well as potential transmission dynamics.

METHODS: A total of 463 K. pneumoniae genomes were included from collected samples and public databases. All genomes underwent comprehensive analysis, including pan-genome profiling, multi-locus sequence typing (MLST), annotation of virulence factors, AMR genes, plasmids, and MGEs, as well as SNP distance-based analysis to infer transmission dynamics, using established bioinformatic tools.

RESULTS: K. pneumoniae isolates exhibited diverse virulence determinants. Hypervirulent isolates were primarily associated with ST23 and ST86, and commonly harbour aerobactin, salmochelin, and rmpA. The majority of isolates were predicted to be MDR, with those from Southeast Asia showing a higher relative abundance of AMR genes associated with the antibiotic classes examined in this study. Among all isolates, the predominant carbapenemase-associated gene was blaNDM-1. Col440I_1 was the most prevalent plasmid replicon, although it did not co-occur with any AMR genes. Association between the IncFII_1_pKP9 plasmid replicon and resistance genes sul-5, blaCTX-M, and blaTEM was found. ISSen9 was the dominant MGE, frequently co-occurring with the plasmid replicons IncFIB(K)_1_Kpn3 and IncFII_1_pKP91. Transmission analysis indicated that the highest isolate similarity occurred within MLST and country. However, clustering based on plasmid replicon profiles revealed that some clusters comprised isolates from multiple countries.

CONCLUSION: This study provides a comprehensive analysis of the genomic characteristics and transmission patterns of K. pneumoniae in South and Southeast Asia, contributing to our understanding of its virulence and resistance mechanisms. These findings further suggest that plasmid replicons may play a critical role in shaping transmission dynamics and provide valuable insights to inform future AMR surveillance and control strategies.},
}

@article {pmid40694258,
year = {2025},
author = {Popov, IV and Chikindas, ML and Popov, IV},
title = {Genomic insights into Streptomyces albidoflavus SM254: tracing the putative signs of anti-Pseudogymnoascus destructans properties.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40694258},
issn = {1678-4405},
support = {25-24-00351//Russian Science Foundation/ ; },
abstract = {White-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, has devastated bat populations across North America. Streptomyces albidoflavus SM254 was previously reported to exhibit antifungal activity against this pathogen, but no comprehensive genomic characterization has been performed to date. Here, we analyzed 34 S. albidoflavus genomes, including the antifungal strain SM254 and 33 publicly available references, to investigate its metabolic potential and functional distinctiveness. Using pangenome reconstruction, phylogenomics, average nucleotide identity, and KEGG pathway profiling, we found that S. albidoflavus SM254 shares high nucleotide identity (> 99%) with five closely related strains but displays a unique combination of complete ethanol fermentation capacity and asparagine biosynthesis deficiency. These traits were exclusive to SM254 and may reflect adaptation to the oxygen-limited, nutrient-variable sediment environment. Functional annotation further revealed high completeness in central energy, redox, and stress-response pathways. Although direct antifungal mechanisms remain to be experimentally validated, S. albidoflavus SM254's unique metabolic profile and ecological specialization suggest potential relevance in biocontrol contexts.},
}

@article {pmid40693537,
year = {2025},
author = {Lovell, JT and Walstead, R and Lawrence, A and Stark-Dykema, E and Farnitano, MC and Harder, A and Brůna, T and Barry, K and Goodstein, D and Jenkins, J and Lipzen, A and Boston, L and Webber, J and Chovatia, M and Eichenberger, J and Talag, J and Grimwood, J and Schmutz, J and Kelly, JK and Sweigart, AL and Fishman, L and Willis, JH},
title = {Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70012},
doi = {10.1111/1755-0998.70012},
pmid = {40693537},
issn = {1755-0998},
support = {DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; DEB-1856180//Division of Environmental Biology/ ; },
abstract = {Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.},
}

@article {pmid40690081,
year = {2025},
author = {Li, Y and Yang, X and Su, J and Alwathnani, H and Ye, J and Rensing, C},
title = {Isolation and pan-genome analysis of Acinetobacter junii SC22, a heavy metal(loid)s resistant and plant growth promoting bacterium, from the Zijin Gold and Copper mine.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {40690081},
issn = {1572-8773},
support = {2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; 2024J08083//Natural Science Foundation of Fujian Province/ ; RSP-2024/205//King Saud University/ ; },
abstract = {Excess heavy metals can be toxic to plants and microbes. The application of plant growth promoting bacteria (PGPB) in agriculture has gained global attention for promising sustainable development, including in heavy metals polluted soil. However, the metal resistance and plant growth promoting determinants of strains belonging to the genus Acinetobacter remain poorly understood. Here, we characterize strain SC22, and analyzed the complete genome of strain SC22. The influence of inoculating with this strain on soybean growth by pot experiment was also analyzed. Our results showed that strain SC22 displayed high As(III) and Cu(II) resistance and high IAA production. The presence of operons such as, merRACDT, zntA and 4 znuABC, czcABCD and arsRBCH, and trpRABCDFS encode functions enabling strain SC22 to survive under extremely highly heavy metal contaminated environments and also produce plant hormones. The inoculation of strain SC22 stimulated soybean growth. Strains belonging to the genus Acinetobacter have an open pan-genome, and ArsH encoded on the core genome displayed differences to ArsH encoded on the genome of other Acinetobacter that were isolated from different habitats. These findings suggest the potential use of strain Acinetobacter junii SC22 in bioremediation and subsequent plant growth promotion in heavy metal polluted environments.},
}

@article {pmid40681976,
year = {2025},
author = {Hu, H and Chang, A and Cao, L and Wei, Y and Yu, F},
title = {Identification of Rcr12, a single dominant clubroot resistance gene near Rcr6 on chromosome B3 of Brassica nigra.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {925},
pmid = {40681976},
issn = {1471-2229},
mesh = {*Disease Resistance/genetics ; *Plant Diseases/genetics/parasitology/immunology ; *Mustard Plant/genetics/parasitology ; *Plasmodiophorida/physiology ; *Chromosomes, Plant/genetics ; *Genes, Plant ; *Plant Proteins/genetics ; Chromosome Mapping ; },
abstract = {BACKGROUND: Clubroot disease, caused by the soil-borne protist Plasmodiophora brassicae, is a major threat to Brassica crops worldwide, leading to significant yield losses. Genetic resistance is the most effective and sustainable management strategy; however, the identification and characterization of clubroot resistance (CR) genes remain a challenge, particularly in Brassica nigra. Despite its abundant CR resources, only one CR gene, Rcr6, has been identified in the B genome of B. nigra, leaving much of its genetic potential unexplored. Understanding the genomic distribution and diversity of CR genes in B. nigra is crucial for expanding resistance breeding options, especially for canola (B. napus).

RESULTS: This study identified Rcr12, a single dominant CR gene on chromosome B3 of the highly resistant B. nigra line BRA19278. Using bulked segregant RNA sequencing (BSR-seq) and fine mapping in segregating populations derived from a cross between CR2748 (a susceptible B. nigra line) and BRA19278, together with single-root protoplast-derived isolates (SPIs) of P. brassicae and comparative analysis across multiple reference genomes, we established that Rcr12 is distinct from Rcr6 despite their close physical proximity. Evidence supporting its distinctiveness includes differential resistance patterns against various SPIs, unique SNP marker associations, and pangenomic analyses. Fine mapping refined the Rcr12 locus to a 0.33 Mb region on chromosome B3, containing multiple resistance gene candidates, in contrast to the single candidate identified for Rcr6. This study is the first to report an nucleotide-binding leucine-rich repeat (NLR) cluster-type CR locus near an NLR singleton in Brassica crops, underscoring the evolutionary and functional significance of this gene arrangement.

CONCLUSION: The discovery of Rcr12 expands our understanding of NLR gene organization and its role in host resistance evolution. Beyond advancing clubroot resistance breeding, this discovery lays the groundwork for studying functional interactions between NLR singletons and clusters in plant immunity. Additionally, the use of purified SPIs as a pathogen differentiation tool offers a novel approach to resolving ambiguities in clubroot research, addressing the complexity of host-pathogen interactions and facilitating future investigations, especially with the anticipated release of a new pathogen classification system.},
}

*Disease Resistance/genetics
*Plant Diseases/genetics/parasitology/immunology
*Mustard Plant/genetics/parasitology
*Plasmodiophorida/physiology
*Chromosomes, Plant/genetics
*Genes, Plant
*Plant Proteins/genetics
Chromosome Mapping

@article {pmid40672531,
year = {2025},
author = {Wang, Z and Hou, X and Guo, Z and Lei, X and Peng, M},
title = {Biodegradation of sodium selenite by a highly tolerant strain Rhodococcus qingshengii PM1: Biochemical characterization and comparative genome analysis.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100426},
pmid = {40672531},
issn = {2666-5174},
abstract = {BACKGROUND: Rhodococcus is an important genus of soil bacteria known for its metabolic diversity and environmental adaptability under harsh and contaminated conditions. However, few studies have reported on the selenium metabolism of Rhodococcus species.

RESULTS: Here, we isolated a highly selenite-resistance strain PM1 (up to 100 mM) from a selenium-rich mine in Enshi City. This strain reduced 50 mM sodium selenite by 99 % within 72 h. SEM and XPS revealed that PM1 reduced selenite to selenium nanorods (SeNRs). Phylogenetic analysis identified PM1 as R. qingshengii. The whole genome of strain PM1 was sequenced, and a comparative genome analysis of strain PM1with 64 other genomes of Rhodococcus was performed. Whole genome sequencing identified a total of 97 heavy metal resistance genes in strain PM1. Comparative genomics revealed that Rhodococcus species possess an open pan-genome, indicating adaptability to diverse environments. Genomic analysis revealed a total of 96 putative selenite-reducing proteins in strain PM1. Four gene clusters, involved in the pentose phosphate pathway, iron-sulfur cluster assembly, sulfate reductase cluster, and sulfate transport complex, showed high conservation of sequence identity within these species.

CONCLUSIONS: To our knowledge, this research enhances our understanding of high selenite reduction in strain PM1 at genomic level and elucidates the biotechnological applications of selenite-reducing bacteria in environmental remediation.},
}

@article {pmid40671251,
year = {2025},
author = {Okumura, K and Ogura, K and Hashimoto, W},
title = {Distribution of Iron Importers and Ecological Traits in Pseudomonas Species Highlights the Potential Role of Efe System in Plant-Related Environments.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70128},
doi = {10.1111/1462-2920.70128},
pmid = {40671251},
issn = {1462-2920},
support = {23K18062//the Japan Society for the Promotion of Science/ ; JPMJSP2110//Japan Science and Technology Agency/ ; },
mesh = {*Iron/metabolism ; *Pseudomonas/genetics/metabolism/classification ; Phylogeny ; *Bacterial Proteins/genetics/metabolism ; Siderophores/genetics/metabolism ; Plant Roots/microbiology ; Genome, Bacterial ; *Plants/microbiology ; Multigene Family ; },
abstract = {Iron is essential for bacterial survival; however, the relationship of Pseudomonas species between iron import systems and environmental adaptation remains poorly understood. Multi-locus sequence and pan-genome analyses using 320 Pseudomonas genomes classified the species into four groups: P. aeruginosa, P. putida, P. syringae, and P. fluorescens, each exhibiting distinct patterns of iron importer and siderophore synthetic gene cluster. The P. aeruginosa group contained fewer iron importers, whereas the P. putida group exhibited a higher prevalence of xenosiderophore importers. The Fe[2+]-importing Efe system was predominantly detected in the P. syringae and P. fluorescens groups, both of which include plant pathogens and plant growth-promoting rhizobacteria. Reanalysis of publicly available transcriptome data revealed efeU, foxA, and fpvA were significantly upregulated in plant roots but not in insect hosts, and these genes were specifically suppressed during plant immune responses. Growth test and in planta competitive assay using P. fluorescens wild-type and Efe system-deficient mutant suggested that the Efe system gives an advantage under plant-related environments. Phylogenetic analysis indicated the Pseudomonas Efe system was inherited through vertical gene transfer from a common ancestor. Our comprehensive analysis revealed the distribution of iron importers across Pseudomonas groups, highlighting the importance of these systems in environmental adaptation.},
}

*Iron/metabolism
*Pseudomonas/genetics/metabolism/classification
Phylogeny
*Bacterial Proteins/genetics/metabolism
Siderophores/genetics/metabolism
Plant Roots/microbiology
Genome, Bacterial
*Plants/microbiology
Multigene Family

@article {pmid40667268,
year = {2025},
author = {Brose, J and Martin, D and Wang, YW and Wood, JC and Vaillancourt, B and Hamilton, JP and Buell, CR},
title = {An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.26.661617},
pmid = {40667268},
issn = {2692-8205},
abstract = {Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A , a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.},
}

@article {pmid40667000,
year = {2025},
author = {Hsieh, P and Soisangwan, N and Gordon, DS and Javidh, A and Harvey, WT and Porubsky, D and Hoekzema, K and Baker, C and Munson, KM and Kinipi, C and Leavesley, M and Brucato, N and Cox, MP and Ricaut, FX and Gallego Romero, I and Eichler, EE},
title = {A global map for introgressed structural variation and selection in humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.661368},
pmid = {40667000},
issn = {2692-8205},
abstract = {Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs ≥50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.},
}

@article {pmid40631289,
year = {2025},
author = {Huete, SG and Coullin, K and Chapeaublanc, E and Torchet, R and Benaroudj, N and Picardeau, M},
title = {Linking genomic evolutionary transitions to ecological phenotypic adaptations in Spirochaetes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40631289},
issn = {2692-8205},
abstract = {Understanding the genetic basis of ecological adaptation is a fundamental challenge of evolutionary biology, often limited by the availability of diverse and curated datasets. Spirochaetes are widely distributed, ancient bacteria found in diverse environments, offering a unique opportunity to explore ecological transitions. Despite their high diversity and the presence of globally important pathogens such as syphilis (Treponema spp.), Lyme disease (Borrelia spp.), or leptospirosis (Leptospira spp.), Spirochaetes remain poorly characterized as a phylum. Moreover, the recent discovery of non-spiral lineages has broadened its complexity and require a re-evaluation of the entire phylum's evolution. Here, we present the most comprehensive phylogenomic and functional analysis of Spirochaetes, examining a curated dataset of 172 spirochaetal genomes representing all cultivable spirochete species. Our robust phylogenetic framework revisits the evolutionary rooting of this phylum and reveals that the Last Spirochaetal Common Ancestor (LSCA) diverged into two major clades, with Brachyspira species diverging early from the rest of Spirochaetes. Ancestral genome reconstruction showed that the LSCA was a motile, endoflagellated bacterium with a heterotrophic metabolism, shedding light on the biology of one of the most anciently diverging bacterial phyla. Functional analysis revealed genomic signatures associated with key phenotypic adaptations within Spirochaetes, such as independent loss of the characteristic spiral morphology and emergence of host-associated lineages. Notably, we found that loss of endoflagellar genes correlated with the appearance of non-spiral species. Lastly, we employed phylogenetic profiling to identify previously uncharacterized motility-associated gene families, whose role was then demonstrated experimentally. Overall, this study provides new evolutionary insights into how ecological specialization has shaped spirochete genomes, offering a framework to elucidate further the mechanisms driving key evolutionary transitions in this clinically relevant phylum.},
}

@article {pmid40662827,
year = {2025},
author = {Rizzo, N and Cáceres, M and Mäkinen, V},
title = {Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i265-i274},
pmid = {40662827},
issn = {1367-4811},
support = {//European Union's Horizon 2020 research and innovation/ ; 956229//Marie Skłodowska-Curie/ ; 101060011//Marie Skłodowska-Curie/ ; //Helsinki Institute for Information Technology/ ; },
mesh = {*Software ; Humans ; *Sequence Alignment/methods ; Algorithms ; *Genomics/methods ; Telomere/genetics ; },
abstract = {SUMMARY: Sequence-to-graph alignment is a central challenge of computational pangenomics. To overcome the theoretical hardness of the problem, state-of-the-art tools use seed-and-extend or seed-chain-extend heuristics to alignment. We implement a complete seed-chain-extend alignment workflow based on indexable elastic founder graphs (iEFGs) that support linear-time exact searches unlike general graphs. We show how to construct iEFGs, find high-quality seeds, chain, and extend them at the scale of a telomere-to-telomere assembled human chromosome.

Our sequence-to-graph alignment tool and the scripts to replicate our experiments are available in https://github.com/algbio/SRFAligner.},
}

*Software
Humans
*Sequence Alignment/methods
Algorithms
*Genomics/methods
Telomere/genetics

@article {pmid40661756,
year = {2025},
author = {Xu, R and Wang, Z and Chen, Z and Wang, Z and Meng, Q and Li, N and Qin, Y},
title = {The Evolution and expression analysis of USP gene family in Solanum.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1546640},
pmid = {40661756},
issn = {1664-462X},
abstract = {As natural environments degrade and extreme weather events become more frequent, humanity increasingly faces the challenge of producing crops under various complex and adverse conditions. Improving crop adaptability has become crucial. Universal stress proteins (USPs) are a class of small molecular proteins widely found in plants, capable of withstanding various biotic and abiotic environmental stresses, including temperature stress, drought, nutrient deficiency, oxidative imbalance, salt and heavy ion toxicity, and pathogenic infections. Enhancing our understanding of USPs holds significant potential for improving plant stress resilience. This study focuses on 13 species of Solanum, including cultivated and wild tomatoes, and systematically identified 438 members of the USP gene family through bioinformatics approaches. Phylogenetic analysis reveals that major USP members are conserved within Solanum, with interspecies differences in USP numbers primarily attributed to copy number variation (CNV). Through synteny and homology analyses, we found that USP27 and USP28 are unique to tomatoes, while the homologous gene of USP19 is absent in cultivated tomatoes. Notably, five unique USP genes are present in S. pennellii, which is characterized by its early differentiation and resistance advantages. Ka/Ks analysis indicates that only the USP10/21 homologous gene pair has undergone positive selection in wild tomatoes, while all other genes are subject to strong negative selection. The USPs in Solanum exhibit high consistency in domain characteristics, sequence conservation, and types of promoter regulatory elements, although there are substantial differences in the number of these elements. Utilizing publicly available data, we identified eight USPs that have undergone domestication or improvement selection, particularly noting the tissue-specific expression patterns of domesticated SolycUSP3/28/30. Through graph pangenome analysis, we screened 12 USPs covered by high-confidence structural variants, which primarily disrupt the intron regions of USPs, leading to significant differences in their expression responses to salt stress. We anticipate that these findings will provide a theoretical foundation and prior knowledge for further understanding and application of USP in plants.},
}

@article {pmid40661132,
year = {2025},
author = {Liu, L and Shu, Y and Wang, Y and Liu, M and Xu, S and Lu, X and Zhang, Y and Yu, L and Tao, Z and Wang, J and Ge, B and Cui, P and Wu, C and Huang, J and Yan, K and Zheng, C and Yang, G and Tian, X and Zhang, S},
title = {The pan genome analysis of WOX gene family in apple and the two sides of MdWUS-1 in promoting leaf-borne shoot.},
journal = {Horticulture research},
volume = {12},
number = {8},
pages = {uhaf117},
pmid = {40661132},
issn = {2662-6810},
abstract = {Unlike animals, plants are sessile organisms that cannot move freely in response to fluctuating and complex environments. As a result, plant development follows post-embryonic processes, enabling flexible developmental strategies to adapt to changing environment. The WUSCHEL-related homeobox (WOX) gene family plays a crucial role in regulating these post-embryonic processes in plants. In this study, we performed an evolutionary analysis of the WOX gene family across 29 plant species, isolating a total of 330 WOX family genes. Our study identified a fern protein with similar length and conserved motifs to WUS gene of spermatophyte, suggesting that the modern clade of the WOX family may have already diverged in ferns. Furthermore, we conducted a pan-genome analysis of the WOX family in Malus, examining the number and gene characteristics of WOX family members across eight varieties. The promoter elements of WUS-1, WUS-2, WOX5-1, and WOX5-2 in different Malus varieties were analyzed further. Additionally, we examined the expression patterns of modern clade WOX family members in developing tissues and during leaf-borne shoot regeneration of Malus. We developed the transgenic lines with inducible overexpression of MdWUS-1 or MdWOX5-1, which revealed that mild upregulation of MdWUS-1 significantly promoted leaf-borne shoot formation, while strong upregulation of MdWUS-1 led to browning and death of explants, likely due to oxidative stress. These findings provide new insights into the evolution of the WOX gene family from ferns into seed plants and lay the foundation for further studies on the spatiotemporal regulation of gene expression during shoot regeneration.},
}

@article {pmid40659765,
year = {2025},
author = {Mondol, SM and Islam, MR and Mia, ME and Hassan, MH and Farhad, F and Akter, K and Shakil, SK and Islam, I and Rakhi, NN and Mustary, JF and Amiruzzaman, and Rahaman, MM},
title = {Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25445},
pmid = {40659765},
issn = {2045-2322},
mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification/pathogenicity ; Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; Bangladesh/epidemiology ; *Burns/microbiology/complications ; *Pseudomonas Infections/microbiology/epidemiology/drug therapy ; *Wound Infection/microbiology/epidemiology ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Genomics ; Genome, Bacterial ; Male ; Female ; },
abstract = {The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa represents a significant challenge in managing nosocomial infections, particularly in vulnerable populations such as burn patients. This study provides genomic and molecular characterization of MDR and XDR P. aeruginosa strains isolated from burn patients at Sheikh Hasina National Institute of Burn and Plastic Surgery (SHNIBPS) in Dhaka, Bangladesh. Over an 8-month period, 110 wound swabs were collected, with 91 isolates identified as P. aeruginosa. Antimicrobial susceptibility testing demonstrated a multidrug-resistant pattern in 30 isolates and an extensive drug-resistant pattern in the remaining 61 isolates analyzed in this study. PCR assays detected beta-lactamase genes from all four Ambler classes, revealing a notable prevalence of blaNDM-1 (16.48%) and blaVIM-2 (31.87%), with both genes co-occurring in 3.30% of the isolates. Additionally, blaPER-1 (15.38%), blaCTX-M (4.40%), blaOXA-1 (84.62%), and blaOXA-48 (51.65%) genes were detected. Class I integrons were detected in 84 isolates. A total of 21% of the isolates exhibited strong biofilm-forming capabilities. Key biofilm-associated genes (pelB, pilT, rhlB) were detected in most of the isolates. Whole genome sequence analysis of two selected XDR isolates identified different beta-lactamase genes such as blaPDC-98, blaPDC-374, blaOXA-50, blaOXA-677 and blaOXA-847. Virulence factor genes, metal resistance genes, and prophage sequences were also identified in the analysis. The genomic epidemiology analysis of 9,055 P. aeruginosa strains, based on MLST data, revealed the dominance of ST235. The blaPDC and blaOXA genes were found to be notably prominent worldwide. The comparative genomic analysis of P. aeruginosa strains from Bangladesh demonstrated an expanding pangenome as well as high degree of genetic variability. The study emphasized the dynamic nature of the P. aeruginosa pangenome and underscored the necessity for stringent infection control measures in burn units to manage and mitigate the spread of these highly resistant strains.},
}

*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification/pathogenicity
Humans
*Drug Resistance, Multiple, Bacterial/genetics
Bangladesh/epidemiology
*Burns/microbiology/complications
*Pseudomonas Infections/microbiology/epidemiology/drug therapy
*Wound Infection/microbiology/epidemiology
beta-Lactamases/genetics
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology
Genomics
Genome, Bacterial
Male
Female

@article {pmid40657825,
year = {2025},
author = {Bai, Y and Luo, X and Qian, W and Geng, X and Bi, X and Zhang, Y},
title = {Identification and Analysis of the AP2/ERF Gene Family in Barley Based on Pan-Genome and Pan-Transcriptome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05138},
pmid = {40657825},
issn = {1520-5118},
abstract = {AP2/ERF gene family is an important family of plant transcription factors, widely involved in various life activities. This study systematically identified the AP2/ERF gene family in 76 barley genomes based on the barley pan-genome, revealing a total of 22,681 family members. Through orthologous gene group analysis, these genes were categorized into 383 orthologous gene groups (OGGs), with core and noncore genes identified. The results indicate that the AP2/ERF gene family in barley cultivars and landraces exhibits greater genetic diversity compared to wild barley, while wild barley is enriched in noncore genes and subjected to stronger selective pressures. Furthermore, two significant AP2/ERF genes, HvTEM1 and HvCRF4, were uncovered through selective pressure analysis, with pan-genome analysis suggesting their important roles in barley reproduction. This is the first pan-genomic analysis of the AP2/ERF gene family in barley, which reveals the evolutionary patterns and functional characteristics of the family in different barley categories. The findings provide new theoretical insights for the genetic improvement and precision breeding of barley.},
}

@article {pmid40655353,
year = {2025},
author = {Manoharan, RS and Raghavan, K and Jayalakshmi, M},
title = {Genomic Diversity and Antimicrobial Resistance of Acinetobacter sp.-A Pan Genome Analysis.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1028-1036},
pmid = {40655353},
issn = {0046-8991},
abstract = {UNLABELLED: Acinetobacter baumannii has been associated with severe clinically acquired infections. The prevalence of non-A. baumannii-linked diseases is now equivalent to that of A. baumannii-associated illnesses. Hence, this study intends to explore the genomic linkage of virulence and antibiotic resistance amongst the five Acinetobacter spp. (A. baumannii, A. haemolyticus, A. johnsonni, and A. nosocomialis) using pan genome analysis. The results revealed open pan genome in Acinetobacter sp. with increase in number of additional genes in pan genome. The resistance gene identifier revealed that A. baumannii was resistant to macrolides, fluoroquinolone, lincosamide, carbapenem, cephalosporin, tetracycline, rifamycin, diaminopyrimidine, phenicol antibiotics, and penem. Non-A. baumannii sp. A. haemolyticus had the Oxa beta lactamase gene (Oxa) with resistance to carbapenem, cephalosporin, penem. A. johnsonii had no perfect hits for resistance but showed weak similarity to Oxa. A. nosocomialis had resistance genes to fluoroquinoids. The prevalence of Acinetobacter baumannii AbaQ gene was found with A. calcoaceticus and A. nosocomialis sequences used in this study supporting the transformation of resistance genes between Acinetobacter sp. This comparative research underlines the need of differentiating between distinct Acinetobacter sp. infections with their genetic profile for accurate diagnosis and management based on their anti microbial resistance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01411-6.},
}

@article {pmid40655291,
year = {2025},
author = {Song, Y and Jo, E and Kim, M and Lee, H and Cha, J},
title = {Harnessing genomic insights to identify antimicrobial traits in Bacillus velezensis MJ06 from Korean soybean-fermented Meju.},
journal = {Food science and biotechnology},
volume = {34},
number = {12},
pages = {2855-2865},
pmid = {40655291},
issn = {2092-6456},
abstract = {UNLABELLED: Bacillus velezensis, a key microorganism in traditional Korean soybean-fermented foods such as Meju, contributes to flavor and food safety. In this study, B. velezensis strains were isolated from Meju, and their morphological characteristics and biosynthetic gene clusters were analyzed using whole-genome sequencing. Pangenome analysis identified core and accessory genes, with MJ06 showing the highest number of genes associated with secondary metabolite biosynthesis, transport, and catabolism. Antimicrobial assays against six foodborne pathogenic bacteria and six fungi revealed MJ06 had the strongest antimicrobial activity, correlating with its enriched secondary metabolite biosynthetic gene clusters. Active antimicrobial compounds were extracted using C18 cartridges and anion exchange chromatography, and liquid chromatography-mass spectrometry analysis identified surfactin and bacillomycin D as major bioactive metabolites. This study highlights the power of comparative genomics in linking genetic potential to functional antimicrobial traits, facilitating the targeted selection of industrially valuable strains for food safety applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-025-01901-3.},
}

@article {pmid40654946,
year = {2025},
author = {Canalda-Baltrons, A and Silcocks, M and Hall, MB and Theys, D and Chang, X and Viberg, LT and Sherry, NL and Coin, L and Dunstan, SJ},
title = {Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.07.652570},
pmid = {40654946},
issn = {2692-8205},
abstract = {Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (Mtb), remains a major global health concern. In this study, we harness long-read sequencing technologies and genome graph tools to construct a Mtb pangenome reference graph (PRG) from 859 high-quality, diverse, long-read assemblies. To enable accurate genotyping of SVs leveraging the PRG, we developed miniwalk , a tool that outperforms a traditional linear genome-based approach in precision for SV detection. We characterize patterns of structural variation genome-wide, revealing a virulence-associated ESX-5 deletion to be recurrent across the phylogeny, and fixed in a sub-lineage of L4. Systematic screens for additional genes that are recurrently affected by SVs implicated those related to metal homeostasis, including a copper exporter fixed in the widely distributed L1.2.1 sub-lineage. Lastly, we genotyped 41,134 isolates and found SVs putatively associated with resistance to various first and second-line drugs. These findings underscore the broader role of SVs in shaping Mtb diversity, highlighting their importance in both understanding evolution and designing strategies to combat drug-resistant TB.},
}

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}

@article {pmid40651546,
year = {2025},
author = {Tang, J and Hu, Z and Zhang, X and Mou, Q and Du, L and Daroch, M},
title = {Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108408},
doi = {10.1016/j.ympev.2025.108408},
pmid = {40651546},
issn = {1095-9513},
abstract = {Parasynechococcus is one of the two essential alongside Prochlorococcus photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate Parasynechococcus species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in Parasynechococcus genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of Parasynechococcus from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.},
}

@article {pmid40650755,
year = {2025},
author = {Sholeh, M and Hamidieh, F and Beig, M and Badmasti, F},
title = {Unravelling the genomic landscape of Acinetobacter baumannii: deep dive into virulence factors, resistance elements, and evolutionary adaptations.},
journal = {Molecular genetics and genomics : MGG},
volume = {300},
number = {1},
pages = {68},
pmid = {40650755},
issn = {1617-4623},
mesh = {*Acinetobacter baumannii/genetics/pathogenicity/drug effects ; *Virulence Factors/genetics ; *Genome, Bacterial/genetics ; Evolution, Molecular ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Acinetobacter Infections/microbiology ; Virulence/genetics ; Phylogeny ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Acinetobacter baumannii presents a major global health threat, particularly in hospital settings. Understanding the genomic landscape of A. baumannii is essential to elucidate its virulence mechanisms, resistance profiles, and evolutionary adaptations, which are critical for developing novel therapeutic strategies. This study aims to comprehensively analyze the pan-genome, antimicrobial resistance (AMR) genes, virulence factors, and clonal relationships of A. baumannii, with the goal of uncovering insights into its pathogenicity and genomic evolution. A total of 27,884 A. baumannii genomes were retrieved from GenBank for analysis. Genome annotation was carried out using Prokka, and pan-genome analysis was performed with Roary. AMR genes and virulence factors were identified through AMRFinderPlus and the Virulence Factor Database via Abricate. Temporal trends in AMR and virulence were analyzed statistically to assess changes over time. The study found that A. baumannii possesses a stable core genome and a highly diverse accessory genome, suggesting an open pan-genome structure. Temporal analysis revealed a significant increase in AMR genes, including blaOXA-23, blaNDM-1, and pmrCAB. Virulence genes were widely distributed across strains, with the sequence types (ST) like ST2[Pas] clone exhibiting global dissemination, highlighting the strain's potential for widespread pathogenicity. This comprehensive genomic analysis of A. baumannii reveals its significant genomic diversity and adaptability, underscoring the critical role of both core and accessory genomes in shaping its pathogenicity and resistance mechanisms. The increasing prevalence of key AMR genes, alongside the widespread dissemination of virulent clones, highlights the urgent need for enhanced surveillance and novel therapeutic strategies to control the spread of this global pathogen. Future research should focus on the functional characterization of resistance and virulence factors to better understand their roles in pathogenicity and to facilitate the development of targeted interventions against A. baumannii.},
}

*Acinetobacter baumannii/genetics/pathogenicity/drug effects
*Virulence Factors/genetics
*Genome, Bacterial/genetics
Evolution, Molecular
*Drug Resistance, Multiple, Bacterial/genetics
Humans
Acinetobacter Infections/microbiology
Virulence/genetics
Phylogeny
Genomics/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40650105,
year = {2025},
author = {Zhou, C and Wang, H and Zhu, X and Li, Y and Zhang, B and Tadege, M and Wu, S and Qi, Z and Xia, Z},
title = {Functional Genomics: From Soybean to Legume.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40650105},
issn = {1422-0067},
support = {2022YFE0130300)//National Key R&D Program (NKP)/ ; U21A20215//National Natural Science Foundation of China/ ; 32272094)//National Natural Science Foundation of China/ ; XDA28070400//Chinese Academy of Sciences/ ; },
mesh = {*Glycine max/genetics ; *Genomics/methods ; *Genome, Plant ; *Fabaceae/genetics ; Gene Editing ; },
abstract = {The Fabaceae family, the third-largest among flowering plants, is nutritionally vital, providing rich sources of protein, dietary fiber, vitamins, and minerals. Leguminous plants, such as soybeans, peas, and chickpeas, typically contain two to three times more protein than cereals like wheat and rice, with low fat content (primarily unsaturated fats) and no cholesterol, making them essential for cardiovascular health and blood sugar management. Since the release of the soybean genome in 2010, genomic research in Fabaceae has advanced dramatically. High-quality reference genomes have been assembled for key species, including soybeans (Glycine max), common beans (Phaseolus vulgaris), chickpeas (Cicer arietinum), and model legumes like Medicago truncatula and Lotus japonicus, leveraging long-read sequencing, single-cell technologies, and improved assembly algorithms. These advancements have enabled telomere-to-telomere (T2T) assemblies, pan-genome constructions, and the identification of structural variants (SVs) and presence/absence variations (PAVs), enriching our understanding of genetic diversity and domestication history. Functional genomic tools, such as CRISPR-Cas9 gene editing, mutagenesis, and high-throughput omics (transcriptomics, metabolomics), have elucidated regulatory networks controlling critical traits like photoperiod sensitivity (e.g., E1 and Tof16 genes in soybeans), seed development (GmSWEET39 for oil/protein transport), nitrogen fixation efficiency, and stress resilience (e.g., Rpp3 for rust resistance). Genome-wide association studies (GWAS) and comparative genomics have further linked genetic variants to agronomic traits, such as pod size in peanuts (PSW1) and flowering time in common beans (COL2). This review synthesizes recent breakthroughs in legume genomics, highlighting the integration of multi-omic approaches to accelerate gene cloning and functional confirmation of the genes cloned.},
}

*Glycine max/genetics
*Genomics/methods
*Genome, Plant
*Fabaceae/genetics
Gene Editing

@article {pmid40644951,
year = {2025},
author = {Gao, M and Pradhan, AK and Blaustein, RA},
title = {Genomic diversity of Cronobacter sakazakii across the food system to consumers at the global scale.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111335},
doi = {10.1016/j.ijfoodmicro.2025.111335},
pmid = {40644951},
issn = {1879-3460},
abstract = {Understanding how foodborne pathogens adapt to changing environments is essential for improving food safety monitoring and control. Cronobacter sakazakii, a persistent opportunistic pathogen associated with powdered infant formula outbreaks, poses critical health risks to neonates and other vulnerable populations. This study tested the hypothesis that genetic variation in C. sakazakii correlates with specific isolation sources and geographic origins across the global food system. We conducted a pangenomics meta-analysis of C. sakazakii derived from food, environmental, and clinical sources spanning North America, Asia, and Europe. A robust fine-tuned Generative Pre-trained Transformer (GPT) model was developed to standardize the categorization of isolate metadata descriptors. C. sakazakii genome assemblies (n = 748) were used to build and annotate the pangenome, and genome size and accessory gene profiles were found to be significantly associated with source type and continent of origin. Isolates from powdered foods, compared to those sourced from alternative foods, had larger genomes and were enriched in functions annotated to Clusters of Orthologous Genes (COG) category L for DNA replication, recombination and repair (e.g., transposase, integrase), among other features. Random forest models using both accessory genes and the subset of virulence factor homologs accurately predicted source attributions, identifying type VI secretion system and heavy metal response genes as key indicators of isolate origins. Several antimicrobial resistance genes associated with efflux (i.e., arlR, facT, oprZ) also exhibited patterns for biogeography. Overall, this study uncovered the distribution of key accessory genetic elements of C. sakazakii throughout the food system, revealing putative adaptations for its persistence and transmission. Our reproducible and automated workflow has potential applications in molecular surveillance for emerging food safety concerns.},
}

@article {pmid40643664,
year = {2025},
author = {Kallscheuer, N and Kumar, G and Ahamad, S and Duddeda, S and Sasikala, C and Jogler, C and Ramana, CV},
title = {Description of Stieleria mannarensis sp. nov., isolated from a marine sponge, and proposal to include members of the genus Roseiconus in the genus Stieleria.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {8},
pages = {111},
pmid = {40643664},
issn = {1572-9699},
support = {239748522//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; BT/HRD/35/01/02/2015//Rajiv Gandhi Centre for Biotechnology, Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/HRD/35/01/02/2015//Rajiv Gandhi Centre for Biotechnology, Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Porifera/microbiology ; Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Fatty Acids/analysis ; DNA, Bacterial/genetics/chemistry ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; },
abstract = {A pink-coloured, salt- and alkali-tolerant strain, JC639[T], was isolated from a specimen of the marine sponge Spheciospongia sp. The novel isolate is motile, aerobic and forms oval to pear-shaped cells. It shares the highest 16S rRNA gene sequence identity with Stieleria neptunia Enr13[T] and Stieleria maiorica Mal15[T] in the family Pirellulaceae (phylum Planctomycetota). Optimum pH and temperature for growth are 8.0 (range 7.0-10.0) and 25 °C (range 10-30 °C), respectively. Major fatty acids are C15:1ω8c, C16:0, C18:1ω9c, C18:0, and C16:1ω7c/C16:1ω6c. Major polar lipids are phosphatidylcholine and phosphatidylethanolamine. The genome of strain JC639[T] has a size of 9.56 Mb and a DNA G + C content of 59.5%. The polyphasic analysis of the isolate supports its delineation from the known species in the genus Stieleria. We therefore introduce Stieleria mannarensis sp. nov., represented by JC639[T] (= KCTC 72168[T] = NBRC 113878[T]) as the type strain. Based on an analysis of established phylogenomic markers performed with all current members of the overlapping genera Stieleria and Roseiconus, we further propose to include the two so far characterized Roseiconus species in the genus Stieleria.},
}

*Porifera/microbiology
Animals
Phylogeny
RNA, Ribosomal, 16S/genetics
Base Composition
Fatty Acids/analysis
DNA, Bacterial/genetics/chemistry
Bacterial Typing Techniques
Sequence Analysis, DNA

@article {pmid40641648,
year = {2025},
author = {Du, ZZ and He, JB and Jiao, WB},
title = {Plant graph-based pangenomics: techniques, applications, and challenges.},
journal = {aBIOTECH},
volume = {6},
number = {2},
pages = {361-376},
pmid = {40641648},
issn = {2662-1738},
abstract = {Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies in plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating the molecular breeding of crops. Conventional methods for genomic analysis typically rely on small variants, such as SNPs and indels, and use single linear reference genomes, which introduces biases and reduces performance in highly divergent genomic regions. By integrating the population level of sequences, pangenomes, particularly graph pangenomes, offer a promising solution to these challenges. To date, numerous algorithms have been developed for constructing pangenome graphs, aligning reads to these graphs, and performing variant genotyping based on these graphs. As demonstrated in various plant pangenomic studies, these advancements allow for the detection of previously hidden variants, especially structural variants, thereby enhancing applications such as genetic mapping of agronomically important genes. However, noteworthy challenges remain to be overcome in applying pangenome graph approaches to plants. Addressing these issues will require the development of more sophisticated algorithms tailored specifically to plants. Such improvements will contribute to the scalability of this approach, facilitating the production of super-pangenomes, in which hundreds or even thousands of de novo-assembled genomes from one species or genus can be integrated. This, in turn, will promote broader pan-omic studies, further advancing our understanding of genetic diversity and driving innovations in crop breeding.},
}

@article {pmid40638214,
year = {2025},
author = {Paintsil, EK and Adu-Asiamah, CK and Boahen, KG and Akenten, CW and Kwarteng, A and Berg, S and Obiri-Danso, K and May, J and Dekker, D and Ofori, LA},
title = {Genomic insights into the diversity, antimicrobial resistance and zoonotic potential of Campylobacter fetus across diverse hosts and geographies.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
pmid = {40638214},
issn = {2057-5858},
mesh = {Animals ; *Campylobacter fetus/genetics/drug effects/classification/isolation & purification/pathogenicity ; Humans ; Cattle ; *Campylobacter Infections/microbiology/veterinary ; Sheep ; Genome, Bacterial ; Genetic Variation ; *Zoonoses/microbiology ; Phylogeny ; Genomics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Reptiles/microbiology ; },
abstract = {Introduction. Campylobacter fetus causes reproductive diseases in livestock and can lead to zoonotic infections such as bacteraemia, particularly in immunocompromised individuals. Despite its significance, its genomic characteristics remain poorly understood. This study analysed 114 publicly available C. fetus genomes to provide global insights into genetic diversity, antimicrobial resistance (AMR) and zoonotic risk.Results. A total of 32 distinct sequence types (STs) were identified across 111 of the 114 C. fetus genomes, spanning 6 continents and diverse hosts (cattle, humans, sheep and reptiles). The majority of strains from cattle (75.6%, n/N=34/45) were assigned to ST-4, which was the most prevalent overall (n=45), while human-associated genomes exhibited the highest diversity with 16 STs. C. fetus subsp. venerealis (Cfv) and its biovar intermedius (Cfvi) genomes clustered closely, forming distinct branches at the biovar level; however, six Cfv genomes were located within Cfvi clades, suggesting a shared ancestry. C. fetus subsp. testudinum (Cft), primarily isolated from humans (60.0%, n/N=18/30), exhibited a more diverse genetic profile, with 20 STs. Cfv from North America and Cfvi from South America formed distinct geographic clusters, while C. fetus subsp. fetus genomes showed no clear geographic patterns, indicating global spread. Pangenomic analysis revealed substantial variation in gene presence/absence in Cft. Five AMR genes were detected, with tet(O) (n=3) being the most common. A total of 220 plasmid contigs were identified across 47 genomes, predominantly in Cfvi (66.8%, n/N=147/220) and Cfv (29.1%, n/N=64/220). Horizontal gene transfer analysis identified 140 genomic islands across 41 genomes, and virulence factor analysis revealed cheY as the sole conserved virulence gene across 35 genomes.Conclusion. These findings provide critical insights into the genomic diversity, zoonotic potential and global distribution of C. fetus, emphasizing the need for integrated genomic and epidemiological strategies to assess its impact on human and animal health.},
}

Animals
*Campylobacter fetus/genetics/drug effects/classification/isolation & purification/pathogenicity
Humans
Cattle
*Campylobacter Infections/microbiology/veterinary
Sheep
Genome, Bacterial
Genetic Variation
*Zoonoses/microbiology
Phylogeny
Genomics
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Reptiles/microbiology

@article {pmid40637797,
year = {2025},
author = {Giani, NM and Lim, SJ and Anderson, LC and Paterson, AT and Engel, AS and Campbell, BJ},
title = {Variation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf074},
pmid = {40637797},
issn = {1574-6941},
abstract = {Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across eight waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of C1 metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.},
}

@article {pmid40637375,
year = {2025},
author = {Salamzade, R and Kottapalli, A and Kalan, LR},
title = {skDER and CiDDER: two scalable approaches for microbial genome dereplication.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
pmid = {40637375},
issn = {2057-5858},
mesh = {*Genomics/methods ; *Software ; *Genome, Bacterial ; *Bacteria/genetics/classification ; *Genome, Microbial ; Phylogeny ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; },
abstract = {An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species or broader taxon, it is often unnecessary and computationally onerous to include all available genomes in studies. In addition, the over-representation of specific lineages due to sampling and sequencing bias can have undesired effects on evolutionary analyses. To assist users with genomic dereplication, we developed skDER and CiDDER (https://github.com/raufs/skDER) to select a subset of representative genomes for downstream comparative genomic investigations. skDER is a nucleotide-based genomic dereplication tool that can dereplicate thousands of microbial genomes leveraging recent advances in average nucleotide identity (ANI) inference. CiDDER dereplicates microbial genomes based on saturation assessment of distinct protein-coding genes. To support usability, auxiliary functionalities are incorporated for testing the number of representative genomes resulting from applying various clustering parameters, automated downloading of genomes belonging to a bacterial species or genus, clustering non-representative genomes to their closest representative genomes and filtering plasmids and phages prior to dereplication. From benchmarking against other ANI-based dereplication tools, skDER, when run in the default mode, was efficient and achieved comparable pangenome coverage and strictly adhered to user-defined cutoffs for both ANI and aligned fraction (AF). Further, we showcase that CiDDER is a convenient alternative to ANI-based dereplication that allows users to more directly optimize the selection of representative genomes to cover a large breadth of a taxon's pangenome.},
}

*Genomics/methods
*Software
*Genome, Bacterial
*Bacteria/genetics/classification
*Genome, Microbial
Phylogeny
Sequence Analysis, DNA/methods
*Computational Biology/methods

@article {pmid40634859,
year = {2025},
author = {Mannan, ABA and Bukharid, MZ and Hossain, MA and Sultana, M},
title = {Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {650},
pmid = {40634859},
issn = {1471-2164},
mesh = {*Arsenic/toxicity/metabolism ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Phylogeny ; *Genome, Bacterial ; *Genomics ; *Microbacterium/genetics/metabolism/drug effects ; Biodegradation, Environmental ; Ecosystem ; *Adaptation, Physiological/genetics ; },
abstract = {BACKGROUND: Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura.

RESULTS: Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as arsC, arsB, and acr3 for arsenic detoxification/transformation, as well as czcD and copB for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of vanY within the vanB cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities. The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane, piperidine, and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis, prodigiosin biosynthesis, and penicillin and cephalosporin biosynthesis, suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential.

CONCLUSION: This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters.},
}

*Arsenic/toxicity/metabolism
*Soil Pollutants/metabolism
*Soil Microbiology
Phylogeny
*Genome, Bacterial
*Genomics
*Microbacterium/genetics/metabolism/drug effects
Biodegradation, Environmental
Ecosystem
*Adaptation, Physiological/genetics

@article {pmid40634784,
year = {2025},
author = {Sharma, R and Chen, C and Zhang, P and Bharti, H and Vikas, VK and Norman, M and Dibley, K and Riaz, A and Hewitt, T and Hoxha, S and Forrest, K and Lagudah, E and Bariana, H and Bansal, U and Hickey, L and Periyannan, S},
title = {Genomic analysis of two all-stage stripe rust resistance genes in the Vavilov wheat landrace AGG40807WHEA1.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {138},
number = {8},
pages = {180},
pmid = {40634784},
issn = {1432-2242},
mesh = {*Triticum/genetics/microbiology ; *Plant Diseases/microbiology/genetics ; *Disease Resistance/genetics ; Basidiomycota ; *Genes, Plant ; Chromosome Mapping ; Genetic Markers ; Polymorphism, Single Nucleotide ; Puccinia ; Chromosomes, Plant/genetics ; },
abstract = {Comparative genomic analysis of two all-stage stripe rust resistance loci from Vavilov wheat landrace accession, AGG40807WHEA1, using Chinese Spring and 10 + hexaploid wheat genomes and validation of closely linked KASP markers. The ongoing occurrence and spread of wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, threatens the global food security. Cultivation of varieties with effective sources of resistance is often followed by the appearance of virulent pathotypes at various times after their introduction. This requires an ongoing search for new sources. Tests of 296 accessions from the Vavilov wheat landrace collection identified numerous lines with broadly effective all-stage stripe rust resistance. Genetic analysis of one of these accessions (Australian Grains Genebank number AGG40807WHEA1) identified two all-stage resistance genes, temporarily named YrV1 and YrV2. The YRV1 and YRV2 loci were mapped to 3.48-3.98 and 730.2-731.2 Mb intervals in the short arm of chromosome 3B and the long arm of chromosome 7B, respectively. A comparative genomic analysis of the YRV1 locus in the Chinese Spring and the 10 + wheat pangenome databases revealed genomic rearrangements and lack of sequences encoding a nucleotide-binding and leucine-rich repeat (NLR) domain protein. Sequences belonging to NLR-like genes were present in the YRV2 region. Kompetitive allele-specific PCR (KASP) markers designed from SNPs IWB71814 and IWB69562, located at 0.4 cM and 0.5 cM distal to YrV1 and YrV2, respectively, were validated for marker-assisted selection using 123 hexaploid and 15 tetraploid wheat and 14 triticale cultivars. YrV1 and YrV2 genes are potentially valuable resources, and use of the closely linked molecular markers will expedite their deployment in breeding.},
}

*Triticum/genetics/microbiology
*Plant Diseases/microbiology/genetics
*Disease Resistance/genetics
Basidiomycota
*Genes, Plant
Chromosome Mapping
Genetic Markers
Polymorphism, Single Nucleotide
Puccinia
Chromosomes, Plant/genetics

@article {pmid40634612,
year = {2025},
author = {Feng, JW and Pidon, H and Cuacos, M and Lux, T and Himmelbach, A and Haghi, R and Fuchs, J and Haberer, G and Kuo, YT and Guo, Y and Jayakodi, M and Toegelová, H and Harpke, D and Knauft, M and Fiebig, A and Maruschewski, M and Ronen, M and Sharon, A and Šimková, H and Mayer, KFX and Spannagl, M and Kumlehn, J and Heckmann, S and Houben, A and Blattner, FR and Stein, N and Mascher, M},
title = {A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634612},
issn = {1476-4687},
abstract = {Wild plants can contribute valuable genes to their domesticated relatives[1]. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes[2]. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.},
}

@article {pmid40634606,
year = {2025},
author = {Zebell, SG and Martí-Gómez, C and Fitzgerald, B and Cunha, CP and Lach, M and Seman, BM and Hendelman, A and Sretenovic, S and Qi, Y and Bartlett, M and Eshed, Y and McCandlish, DM and Lippman, ZB},
title = {Cryptic variation fuels plant phenotypic change through hierarchical epistasis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40634606},
issn = {1476-4687},
abstract = {Cryptic genetic variants exert minimal phenotypic effects alone but are hypothesized to form a vast reservoir of genetic diversity driving trait evolvability through epistatic interactions[1-3]. This classical theory has been reinvigorated by pan-genomics, which is revealing pervasive variation within gene families, cis-regulatory regions and regulatory networks[4-6]. Testing the ability of cryptic variation to fuel phenotypic diversification has been hindered by intractable genetics, limited allelic diversity and inadequate phenotypic resolution. Here, guided by natural and engineered cis-regulatory cryptic variants in a paralogous gene pair, we identified additional redundant trans regulators, establishing a regulatory network controlling tomato inflorescence architecture. By combining coding mutations with cis-regulatory alleles in populations segregating for all four network genes, we generated 216 genotypes spanning a wide spectrum of inflorescence complexity and quantified branching in over 35,000 inflorescences. Analysis of this high-resolution genotype-phenotype map using a hierarchical model of epistasis revealed a layer of dose-dependent interactions within paralogue pairs enhancing branching, culminating in strong, synergistic effects. However, we also identified a layer of antagonism between paralogue pairs, whereby accumulating mutations in one pair progressively diminished the effects of mutations in the other. Our results demonstrate how gene regulatory network architecture and complex dosage effects from paralogue diversification converge to shape phenotypic space, producing the potential for both strongly buffered phenotypes and sudden bursts of phenotypic change.},
}

@article {pmid40633701,
year = {2025},
author = {Mokgokong, SP and Hassim, A and Mafuna, T and Turner, WC and van Heerden, H and Lekota, KE},
title = {Comparative genomics of Bacillus anthracis A and B-clades reveals genetic variation in genes responsible for spore germination.},
journal = {Genomics},
volume = {},
number = {},
pages = {111074},
doi = {10.1016/j.ygeno.2025.111074},
pmid = {40633701},
issn = {1089-8646},
abstract = {Bacillus anthracis, the causative agent of anthrax, is composed of three genetic clades (A, B, and C). Clade-A is the most common and distributed worldwide, B-clade has a narrow geographic distribution, and C-Clade is rare. South Africa's Kruger National Park (KNP) has high diversity of B. anthracis, with strains from A and B clades described from its northernmost region, Pafuri. We employed whole genome sequencing to investigate the genomic diversity of B. anthracis strains isolated from animal carcasses (n = 34) during the 2012-2015 outbreaks. Whole-genome single-nucleotide polymorphism (wgSNP) analysis assigned the 2012-2015 B. anthracis genomes to the A-clade branch, distributed across the branch's two minor sub-clades A.Br.005/006. Additionally, pan-genomic analysis distinguished the A- and B-clade genomes, identifying unique accessory genes. Notable genetic differences include the biosynthetic spore cell wall genes; long-chain fatty acid CoA ligases (FaD13), Bacillus collagen-like protein of anthracis (BclA) involved in the exosporium germination, as well as a truncated murein DD-endopeptidase (mepH) found in the pXO2 plasmid of the B-clade strains. The tryptophan synthase subunit alpha gene (trpA), which results in a pseudogene in B-clade genomes separates the A- and B-clade genomes. These differences in biosynthetic cell wall genes suggest variation in adaptability or cell growth of the B-clade strains in the environment, further influenced by the truncation of the trpA gene involved in spore germination. The A.Br.005/006-clade strains in KNP exhibit higher genetic diversity, which may enhance their resilience to environmental stressors. In contrast, the KNP B-clade (B.Br.001/002) strains show limited genetic variation, potentially reducing their adaptability. This pattern is evident through whole-genome SNP analysis and pan-genomics investigating the evolution of B. anthracis.},
}

@article {pmid40631900,
year = {2025},
author = {Migicovsky, Z},
title = {Genomic resources for crop wild relatives are critical for perennial fruit breeding and conservation.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70068},
doi = {10.1002/ajb2.70068},
pmid = {40631900},
issn = {1537-2197},
abstract = {Many perennial fruit crops are clonally propagated, resulting in uniform fruit quality but increasing vulnerability to pests, diseases, and climate change. In contrast, closely related crop wild relatives (CWRs) continue to evolve in response to these pressures and are a valuable source of adaptive traits. Despite their potential, CWRs are underutilized in perennial fruit breeding. Efficient and accurate introgression of traits from CWRs during perennial fruit breeding will require the use of genomics. Genomics-assisted breeding begins with genetic mapping, such as genome-wide association studies, to identify markers predictive of traits of interest. For diverse species such as CWRs, a pangenomic approach that incorporates multiple species as a reference is often necessary. Continued use of CWRs in fruit breeding also depends on their conservation, both in situ (in natural habitats) and ex situ (off-site). Ex situ collections can also be used for genetic mapping, further supporting genomics-assisted plant breeding efforts. Ultimately, breeding and conservation of perennial fruit crops are complementary goals that benefit from the development and application of genomic resources.},
}

@article {pmid40631467,
year = {2025},
author = {Fan, W and Liao, Z and Gu, M and Zhang, Y and Lei, W and Zhang, Y and Li, H and Yan, J and Xiao, Y and Lin, H and Jin, S and Yu, Y and Fang, J and Ye, N and Wang, P},
title = {Pan-Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma-Related Genes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70013},
doi = {10.1111/1755-0998.70013},
pmid = {40631467},
issn = {1755-0998},
support = {2022YFD2101102//National Key Research and Development Program of China/ ; 2023J01508//Natural Science Foundation of Fujian Province/ ; },
abstract = {Jasmine (Jasminum sambac) is globally renowned for its distinct fragrance and ornamental appeal, existing primarily in three floral morphologies: single-petal, double-petal and multi-petal. De novo sequencing and chromosome-level genome assembly were performed on two distinct jasmine varieties: 'Yuanye' double-petal and 'Bijian' multi-petal jasmines. These assemblies, along with three previously published genomes, were integrated to construct a pan-genome framework that comprehensively encompasses both the core and variable genomic components of jasmine. A substantial number of structural variations (SVs) and single nucleotide polymorphisms (SNPs) had been identified, of which 89.5% were insertions/deletions (size ≥ 50 bp), whereas gene families also exhibited significant contractions and expansions, revealing the high complexity and dynamics of the jasmine genomes. Comparative genomic approaches further revealed multiple transcription factor families associated with aromatic biosynthesis, floral organogenesis and environmental adaptability. Key genes involved in the formation of jasmine scent, with a particular focus on the variation in copy number and expression levels of critical enzyme genes responsible for the production of four major volatile terpenoids and benzyl acetate, thereby elucidating the genetic basis of jasmine aroma diversity. Additionally, within the MADS-box gene family, the PI and AP3 subfamilies are hypothesized to play crucial roles in the development of floral organs. Through the integration of these comprehensive data, a pan-genome website for jasmine was developed to facilitate data download and visualise genomic variations via a genome browser (https://www.pan-jasmine.cn/). In summary, this work provides valuable genomic resources for the genetic enhancement and marker-assisted breeding of jasmine.},
}

@article {pmid40629470,
year = {2025},
author = {Wang, W and Liu, Q and Zhao, Q and Zhu, Z and Wen, W and Zhang, Z and Li, X},
title = {Homologous recombination and evolutionary arms race drive the adaptive evolution of African swine fever virus.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {142},
pmid = {40629470},
issn = {1297-9716},
support = {2023YFD1800500//National Key Research and Development Program of China/ ; JSSCTD202224//Jiangsu Innovative and Entrepreneurial Talent Team Project/ ; D18007//the 111 Project/ ; },
mesh = {*African Swine Fever Virus/genetics/physiology ; *Evolution, Molecular ; *Genome, Viral ; *Homologous Recombination ; Animals ; Swine ; African Swine Fever/virology ; Biological Evolution ; Phylogeny ; },
abstract = {African Swine Fever Virus (ASFV) is a highly contagious pathogen responsible for substantial economic losses in swine populations worldwide. Despite extensive research, the mechanisms underlying the genomic evolution of ASFV remain poorly understood. In this study, we conducted a comprehensive analysis of ASFV evolutionary strategies by examining 252 complete ASFV genomes. Our pan-genome analysis categorizes ASFV genes into core and non-core categories, with core genes predominantly locate in the central region of the genome, while non-core genes are primarily situated at the variable genomic termini, exhibiting higher rates of genetic loss and diversification. Gene synteny analysis revealed that ASFV inherited a portion of its core gene repertoire from the common ancestor of the Asfarviridae family, establishing its central genomic framework, and acquired virus-specific genes that contributed to its distinct genetic identity during divergence. Homologous recombination analysis identified 76 genes exhibiting strong recombination signals, emphasizing the critical role of recombination in ASFV evolution. Additionally, 9 genes were found to be under positive selection, highlighting the influence of the host-virus evolutionary arms race in shaping ASFV genome, particularly in terms of immune evasion and host interaction. These findings underscore the dynamic evolutionary forces driving ASFV adaptive evolution and provide important implications for understanding the virus global spread and the development of effective control measures.},
}

*African Swine Fever Virus/genetics/physiology
*Evolution, Molecular
*Genome, Viral
*Homologous Recombination
Animals
Swine
African Swine Fever/virology
Biological Evolution
Phylogeny

@article {pmid40629160,
year = {2025},
author = {Kundu, P and Thorat, SA and Kiran, A and Goel, K and Zinta, G},
title = {Plant-derived triterpenoid saponins: multifaceted roles and bioengineering prospects.},
journal = {Plant cell reports},
volume = {44},
number = {8},
pages = {172},
pmid = {40629160},
issn = {1432-203X},
support = {MLP-178//CSIR/ ; },
mesh = {*Saponins/metabolism/chemistry/biosynthesis/pharmacology ; *Triterpenes/metabolism/chemistry ; *Plants/metabolism ; *Bioengineering/methods ; Biosynthetic Pathways ; Humans ; },
abstract = {Saponins are plant secondary metabolites synthesized through the triterpenoid biosynthetic pathway by a series of modifications, including acylation, glycosylation, and oxidation of β-amyrin, a product of 2,3-oxidosqualene. They are classified into triterpenoid saponins and steroidal saponins, exhibiting diverse bioactivities and applications in the pharmaceuticals, agriculture, cosmetics, and food industries. Beyond their industrial relevance, saponins play a crucial role in plant defense, stress tolerance, and shaping of rhizosphere microbiota. Despite their significant potential, plant-derived triterpenoid saponins remain underexplored. Additionally, their biosynthesis in plants is limited and requires rigorous exploration to decipher novel biotechnological approaches to enhance their production. In this review, we provide a comprehensive update on the types of triterpenoid saponins, the regulation of their biosynthesis pathway, defense responses, therapeutic activities, biotechnological interventions, and the challenges associated with the large-scale production of saponins. Also, we explicitly provide an update on strategies for synthesizing saponins in microbial cells and in vitro plant systems. Thus, this review provides a foundation for further research on plant-derived triterpenoid saponins, their diverse therapeutic activities, their critical role in defense responses, and the development of novel methods to increase saponin production for human health, industrial, and agricultural applications.},
}

*Saponins/metabolism/chemistry/biosynthesis/pharmacology
*Triterpenes/metabolism/chemistry
*Plants/metabolism
*Bioengineering/methods
Biosynthetic Pathways
Humans

@article {pmid40627207,
year = {2025},
author = {Elufisan, TO and Rosas-García, NM},
title = {Whole genome sequence analysis of pigmented Bacillus inaquosorum LBA001 revealed biosynthetic gene clusters for a variety of secondary metabolites.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {8},
pages = {107},
pmid = {40627207},
issn = {1572-9699},
support = {Apoyos CI//IPN/ ; },
mesh = {*Bacillus/genetics/metabolism/classification/isolation & purification ; Phylogeny ; Whole Genome Sequencing ; *Genome, Bacterial ; *Multigene Family ; *Secondary Metabolism/genetics ; *Pigments, Biological/biosynthesis/genetics ; *Biosynthetic Pathways/genetics ; Soil Microbiology ; Base Composition ; },
abstract = {The strain Bacillus inaquosorum LBA001 was isolated from a soil sample as a potential entomopathogenic bacteria; and produces a brown pigment at each growth on LB (Luria-Bertani) agar. We investigated its biochemical and physiological characteristics using the standard bacteriological technique. The whole genome sequencing was used to explore its genetic composition and metabolic capabilities. We used whole genome sequencing to examine the role of its genetic makeup and its potential metabolic capacity. The whole genome assembly resulted in one scaffold with a GC content of 43.19% and a genome size of about 4.3 Mb. The Prokka annotation showed 4,149 coding sequences and full sets of ribosomal RNA (5S, 16S, and 23S). The pan genome analysis identified 192 core genes among the strains compared with numerous accessory genes in individual strains. Phylogenetic analysis confirmed that it belongs to the B. inaquosorum clade, as it has much in common with B. inaquosorum KCTC 13249[ T]. AntiSMASH indicated that LBA001 contains certain groups of biosynthetic genes such as bacilysin, surfactin, fengycin, bacillaene, and pulcherriminic acid among others. The predicted proteome of LBA001 was subjected to BLAST-based homology searches against reference pigment gene database. The analysis identified 23 high-confidence pigment biosynthesis genes, with five different types of pigments in seven distinct colors. Numerous CAZymes in LBA00 were predicted, suggesting its potential applications in biotechnology and agriculture. The identification of potential antibiotic resistance genes in LBA001 genome reflected its adaptive characteristics. These findings will add to our understanding of B. inaquosorum metabolic versatility and its potential as a beneficial source of bioactive compounds.},
}

*Bacillus/genetics/metabolism/classification/isolation & purification
Phylogeny
Whole Genome Sequencing
*Genome, Bacterial
*Multigene Family
*Secondary Metabolism/genetics
*Pigments, Biological/biosynthesis/genetics
*Biosynthetic Pathways/genetics
Soil Microbiology
Base Composition

@article {pmid40625851,
year = {2025},
author = {Karberg, KA},
title = {The ever-evolving world of microbes: the current state of microbial taxonomy, genome evolutionary dynamics, and the potential impact on the future of agricultural microbials risk assessment.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1620652},
pmid = {40625851},
issn = {2296-4185},
abstract = {Risk assessment frameworks for plant agricultural biotechnology products have been in place for decades, focused on the evaluation of living biotechnology products created through genetic engineering. These products contain genetic material from outside the breeder's gene pool, which is often from different taxa or represents "novel combinations of genetic material". These products are typically considered to be "genetically modified" (GM) organisms in regulatory jurisdictions. However, in the microbial world, particularly among Bacteria and Archaea, the rapid expansion of genome sequence databases shows that natural microbial innovation primarily occurs through the natural exchange of genetic material from various sources, even from different taxa. This means that many microbes can be considered naturally occurring GM organisms. This raises the question of whether labeling a microbe as GM is always scientifically relevant for risk assessment. In most regulatory frameworks, being classified as GM significantly impacts the registration path, especially for microbes intended for environmental release. A more effective and science-based regulatory approach would assess the actual functions of a microbe rather than relying on the uncertain classification of its genetic material. This would benefit regulators, developers, and society by promoting the use of microbial technologies for agricultural use.},
}

@article {pmid40623120,
year = {2025},
author = {Dong, X and Jiao, D and Xue, H and Fan, S and Wei, C},
title = {APAV: An advanced pangenome analysis and visualization toolkit.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013288},
doi = {10.1371/journal.pcbi.1013288},
pmid = {40623120},
issn = {1553-7358},
abstract = {Traditional pangenome analysis focuses on gene presence/absence variations (gene PAVs). However, the current methods for gene PAV analysis are insensitive to detect small but valuable mutations within gene regions, and they overlook variations in intergenic regions. Additionally, the visual inspection of PAVs is an important but time-consuming step for pangenome analysis and result interpretation. To address these issues, we present APAV, an advanced toolkit designed for comprehensive PAV analysis and visualization. It integrates gene element-level PAV analysis and provides PAV analysis for arbitrary given regions in a genome. The resulted PAV profile can be visualized and investigated interactively with reports in HTML format, enabling researchers to conveniently verify sequencing read depth, target region coverage, and intervals of absence for each PAV. Furthermore, APAV offers various subsequent analysis and visualization functions based on the PAV profile table, including basic statistics, sample clustering, genome size estimation, and phenotype association analysis. We demonstrated the capability of APAV with pangenome analysis of tumor genomes and rice genomes. Performing PAV analysis at the element level not only provides more accurate information about the variations but also uncovers a larger number of variations for the phenotype-genotype association studies. In the rice genome analysis, we identified over twenty thousand distributed genes and more than fifty thousand distributed genetic elements. In the tumor genome analysis, element-level analysis revealed approximately three times as many phenotype-related genes as gene-level analysis. This indicates that altering the PAV unit from genes to smaller segments or elements can lead to more biological insights.},
}

@article {pmid40616976,
year = {2025},
author = {González-Cruz, M and Reyes-Gastellou, A and Castelán-Vega, JA and Monterrubio-López, GP and Jiménez-Alberto, A and Aparicio-Ozores, G and Ribas-Aparicio, RM},
title = {In silico development of a broad-spectrum vaccine against ESKAPE pathogens.},
journal = {Journal of molecular graphics & modelling},
volume = {140},
number = {},
pages = {109120},
doi = {10.1016/j.jmgm.2025.109120},
pmid = {40616976},
issn = {1873-4243},
abstract = {Antimicrobial-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) have significantly restricted therapeutic alternatives for critical infections, consequently contributing to increase the severity and mortality of infectious illnesses that represent a significant global health challenge. Vaccination as a preventive measure can be crucial in substantially reducing bacterial infections and is potentially effective against antibiotic-resistant bacteria. This study shows the design of an epitope-based vaccine capable of neutralizing shared antigenic determinants present among the ESKAPE pathogens. The pangenome of the ESKAPE pathogens was analyzed to extract the core proteome. This approach facilitated reverse vaccinology analysis to identify antigenic proteins within this bacterial group. The study revealed similar structures in porins OmpA, OprD, and TolC, as well as the collagen-binding adhesins Acm and Cna. These proteins were then utilized to predict T-cell and B-cell epitopes, selecting those with their best physicochemical properties, antigenicity, non-allergenicity, and lack of toxicity. Additionally, epitopes located on the surface of the antigens and capable of coupling with HLA molecules were prioritized. In this computational approach, we engineered a construct incorporating the adjuvant RS09, a TLR4 agonist, and immunogenic epitopes connected by linkers. We assessed the stability of their interaction with pattern recognition receptors of the immune system through molecular docking and molecular dynamics simulations. The in silico immune simulation demonstrated that the vaccine could trigger humoral and cell-mediated immune responses. The resulting construct potentially represents an effective and safe vaccine candidate to prevent infections caused by the ESKAPE group.},
}

@article {pmid40616241,
year = {2025},
author = {Dhaouadi, S and Vinchira-Villarraga, D and Bijarniya, S and Webster, AJ and Dorati, F and Brady, C and Arnold, DL and Rabiey, M and Jackson, RW},
title = {A Sucrose-Utilisation Gene Cluster Contributes to Colonisation of Horse Chestnut by Pseudomonas syringae pv. aesculi.},
journal = {Molecular plant pathology},
volume = {26},
number = {7},
pages = {e70116},
pmid = {40616241},
issn = {1364-3703},
support = {//JAAB/ ; },
mesh = {*Pseudomonas syringae/genetics/pathogenicity/metabolism/growth & development ; *Sucrose/metabolism ; *Plant Diseases/microbiology ; *Multigene Family/genetics ; *Aesculus/microbiology ; Virulence/genetics ; Plant Leaves/microbiology ; },
abstract = {Pseudomonas syringae pathovar aesculi (E-Pae) causes bleeding canker disease in the woody tissue of European horse chestnut (HC). Comparative genomic analysis of E-Pae with a related leaf-infecting strain (I-Pae) and other P. syringae strains identified candidate virulence genes for colonisation of woody tissue, including a sucrose uptake and utilisation system (scrYABCDBR cluster) found in 162 of 206 P. syringae strains spanning the pangenome. Growth analysis using sucrose as sole carbon source showed that I-Pae (lacking the gene cluster) was unable to grow whereas E-Pae could grow. P. savastanoi pv. phaseolicola 1448A and P. syringae pv. morsprunorum R15244 were compromised in growth despite the presence of the gene cluster. Sucrose utilisation assays using scrB and scrY mutants and complemented strains confirmed the importance of the cluster for sucrose metabolism in vitro. Pathogenicity assays in HC revealed the sucrose gene cluster is important for symptom development in the woody tissue. While the scr genes contribute to disease causation, they were not essential for pathogen fitness when compared to hrpL and hopAB1 mutants. E-Pae caused disease symptoms in HC leaves, suggesting the strain has the potential to infect leaves as well. However, it was notable that the scrB mutant of E-Pae caused increased disease symptoms, possibly highlighting a niche adaptation strategy for I-Pae to cause leaf spots in HC as well as constraining E-Pae to predominantly infect the woody tissue.},
}

*Pseudomonas syringae/genetics/pathogenicity/metabolism/growth & development
*Sucrose/metabolism
*Plant Diseases/microbiology
*Multigene Family/genetics
*Aesculus/microbiology
Virulence/genetics
Plant Leaves/microbiology

@article {pmid40611899,
year = {2025},
author = {Pokharel, SK and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40611899},
issn = {2692-8205},
support = {P20 GM130460/GM/NIGMS NIH HHS/United States ; R01 GM149795/GM/NIGMS NIH HHS/United States ; },
abstract = {A surge in sequenced myxobacteria catalyzed by advancements in long read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze eleven genera and 195 sequenced genomes including ten newly reported myxobacterial isolate, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient, sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.},
}

@article {pmid40608406,
year = {2025},
author = {Ito, K and Ito, Y},
title = {Comparative genomic analysis of Latilactobacillus sakei strains provides new insights into their association with different niche adaptations.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
pmid = {40608406},
issn = {1465-2080},
mesh = {*Genome, Bacterial ; Phylogeny ; *Adaptation, Physiological/genetics ; Plasmids/genetics ; *Latilactobacillus sakei/genetics/classification/physiology/growth & development/metabolism ; Genomics ; Carbohydrate Metabolism/genetics ; Fermentation ; Genetic Variation ; },
abstract = {Latilactobacillus sakei, a lactic acid bacterium in diverse environments such as fermented foods, meat and the human gastrointestinal tract, exhibits significant genetic diversity and niche-specific adaptations. This study conducts a comprehensive comparative genomic analysis of 29 complete L. sakei genomes to uncover the genetic mechanisms underlying these adaptations. Phylogenetic analysis divided the species into three distinct clades that did not correlate with the source of isolation and did not suggest any niche-specific evolutionary direction. The pan-genome analysis revealed a substantial core genome alongside a diverse genetic repertoire, indicating both high genetic conservation and adaptability. Predicted growth rates based on codon use bias analysis suggest that L. sakei strains have an overall faster growth rate and may be able to efficiently dominate in competitive environments. Plasmid analysis revealed a variety of plasmids carrying genes essential for carbohydrate metabolism, enhancing L. sakei's ability to thrive in various fermentation substrates. It was also found that the number of genes belonging to the GH1 family amongst sugar metabolism-related genes present on chromosomes and plasmids varies between strains and that AA1, which is involved in alcohol oxidation, has been acquired from plasmids. blast analysis revealed that some strains have environmental adaptation gene clusters of cell surface polysaccharides that may mediate attachment to food and mucosa. The knowledge gleaned from this study lays a solid foundation for future research aimed at harnessing the genetic traits of L. sakei strains for industrial and health-related applications.},
}

*Genome, Bacterial
Phylogeny
*Adaptation, Physiological/genetics
Plasmids/genetics
*Latilactobacillus sakei/genetics/classification/physiology/growth & development/metabolism
Genomics
Carbohydrate Metabolism/genetics
Fermentation
Genetic Variation

@article {pmid40608125,
year = {2025},
author = {León-Lemus, A and Martínez-García, M and Cabirol, N and Campos, JE and Monsalvo-Reyes, A},
title = {Draft genome sequence and comparative genomic analysis of Halomonas salifodinae strain A2 isolated from the Zapotitlán Salinas Valley, Puebla, Mexico.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {28},
pmid = {40608125},
issn = {1433-4909},
mesh = {*Halomonas/genetics/isolation & purification/classification ; *Genome, Bacterial ; Mexico ; Phylogeny ; },
abstract = {In this study, we report the draft genome sequence of strain A2. The genome size was 3.8 Mbp, the GC content was 67.4%, and it was predicted to contain 3520 protein-coding genes, 62 tRNA genes, 8 rRNA genes, and 4 snRNA genes. Phylogenetic analysis of the 16S rRNA gene in different databases suggests that strain A2 belongs to Halomonas salifodinae. Also, Multilocus Sequence Typing analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic of the core genes and comparative genomic analysis using the Average Nucleotide Identity, digital DNA-DNA Hybridization, Average Amino acid Identity, the Percentage of Conserved Proteins values indicators, and the Genome Taxonomy Database indicates that strain A2 is identified as H. salifodinae and suggest that this species has a closer phylogenetic relationship with the genus Bisbaumannia than with Halomonas. The pangenomic analysis of A2 against 100 reference genomes of described Halomonas and another related genus shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome genes, and 691 unique genes. A2 has 261 signature genes that it shares only with Bisbaumannia and Halomonas salifodinae. For strain A2 we found 29 genes for secretion systems, 23 genes for Na[+] and K[+] ion transport, 6 Biosynthetic Gene Clusters groups, a total of 12 genomic islands, an 8.2 kb gene prophage region, 15 regions associated with CRISPR and one CAS-TypeIF cas gene cluster region, 12 genes of biotechnological importance, 38 unique genes essential for adaptability and biotechnological relevance, as well as, 35 genes for the synthesis of compatible solutes. Comparative genomics analysis shows that strain A2 has multiple unique genetic features that could be useful for biotechnological applications. The result of this study places the species Halomonas salifodinae in a very close relationship with the genus Bisbaumannia than with Halomonas, so its reclassification to the genus Bisbaumannia is proposed for future validation.},
}

*Halomonas/genetics/isolation & purification/classification
*Genome, Bacterial
Mexico
Phylogeny

@article {pmid40601639,
year = {2025},
author = {Tareq, MMI and Biswas, S and Rahman, FA and Siam, LS and Tauhida, SJ and Ahmed, S and Shovon, HJ and Ahmed, M and Jerin, KA and Hasan, MN},
title = {Development of a potential vaccine against Capripox virus implementing reverse vaccinology and pan-genomic immunoinformatics.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326310},
pmid = {40601639},
issn = {1932-6203},
mesh = {*Capripoxvirus/immunology/genetics ; Animals ; *Viral Vaccines/immunology ; Epitopes, T-Lymphocyte/immunology ; Epitopes, B-Lymphocyte/immunology ; Vaccinology/methods ; Computational Biology/methods ; *Poxviridae Infections/prevention & control/immunology/veterinary/virology ; *Vaccine Development ; Sheep ; Goats ; Viral Proteins/immunology/chemistry/genetics ; Immunoinformatics ; },
abstract = {CPXV is responsible for animal diseases affecting cattle (Lumpy Skin Disease), sheep (Sheeppox), and goats (Goatpox). During outbreaks, these diseases have huge socio-economic effects. Now, no vaccination that is effective against sheeppox, goatpox, and lumpy skin disease is available. This work used an immunoinformatic methodology to discover possible targets for vaccination against CPXV. After the 122 CPXV proteins were obtained from the Vipr database, several investigations into the proteins' virulence, antigenicity, toxicity, solubility, and IFN-g activity were carried out. Three outer membrane and extracellular proteins were selected to predict their B-cell and T-cell epitopes based on certain distinctive features. These epitopes exhibit conservation across three species, namely Sheeppox virus (SPPV), Goatpox virus (GTPV), and Lumpy skin disease virus (LSDV) of CPXV. This will provide more comprehensive immunity against diverse virus strains worldwide. Nine MHC-I, MHC-II, and B-cell epitopes were selected to generate multi-epitope vaccine constructions. These constructs were linked using AAY, GPGPG, and KK linkers and 50S ribosomal protein L7/L12 adjuvants to enhance the immunogenicity of the vaccines. Molecular modeling and structural validation enabled the production of vaccine constructs with high-quality 3D structures. CPXV (Protein A35, Protein Resolve A22, and Scaffold Protein) was selected for further analysis because of its varied immunological and physiochemical properties (Number of Amino Acids, Molecular Weight (Daltons), Theoretical pI Aliphatic index, Grand average of hydropathicity (GRAVY), Instability index GC content, and CAI value) and docking scores. The bacterial expression system showed notable gene expression for the CPXV-V5 vaccine, as shown by computational cloning analysis. Molecular dynamics (MD) simulations revealed structural stability and long-term epitope visibility, implying strong immune responses after delivery. These results suggest that the developed vaccines might be quite safe and effective in practical settings, and they offer a solid foundation for further experimental verification.},
}

*Capripoxvirus/immunology/genetics
Animals
*Viral Vaccines/immunology
Epitopes, T-Lymphocyte/immunology
Epitopes, B-Lymphocyte/immunology
Vaccinology/methods
Computational Biology/methods
*Poxviridae Infections/prevention & control/immunology/veterinary/virology
*Vaccine Development
Sheep
Goats
Viral Proteins/immunology/chemistry/genetics
Immunoinformatics

@article {pmid40600140,
year = {2025},
author = {Shahed, K and Islam, SI and Sangsawad, P and Jung, WK and Permpoonpattana, P and Linh, NV},
title = {Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537826},
pmid = {40600140},
issn = {1664-302X},
abstract = {Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.},
}

@article {pmid40598134,
year = {2025},
author = {He, RS and Zhao, R and Lin, JJ and Li, Y and Kong, XZ and Xu, JX and Wu, JH and Bu, XJ and Zhang, YJ and Sun, Y},
title = {Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {195},
pmid = {40598134},
issn = {1741-7007},
support = {31871964, 31801738, 32302320//National Natural Science Foundation of China/ ; CARS-01-40//National Rice Industry Technology System Project/ ; 202003a06020009//Major Science and Technology Projects in Anhui Province/ ; },
mesh = {Animals ; *Takifugu/genetics/physiology ; *Genome ; *Genetic Variation ; *Animal Migration ; Gene Flow ; },
abstract = {BACKGROUND: The genus Takifugu includes highly valued fish species known for their delicate flavor, making them popular in multiple countries. However, many species from this genus face significant threats. In order to better understand the genetic diversity and evolutionary dynamics of Takifugu, a syntelog-based pan-genome and graph genome were constructed using the data of seven Takifugu species.

RESULTS: The analysis of 28,085 syntelog groups (SGs) composed of protein-coding genes revealed that only 57.3% of the SGs were shared among all individuals, whereas the remaining genes presented presence-absence variation (PAV) across the seven genomes. Using the graph genome as a reference, a population of 160 Takifugu individuals was analyzed, from which 20,133,471 SNPs, 4,606,141 Indels, and 152,200 SVs were identified. The gene flow analysis revealed directional gene flow from Takifugu bimaculatus and Takifugu flavidus to Takifugu oblongus. Notably, a 51-bp insertion in the ABCB9 gene differed significantly in frequency between the two migratory populations, suggesting the potential role of this gene in the migratory behavior of these species. Additionally, the expression profiles from 13 tissues or organs (brain, gallbladder, gill, gonad, heart, kidney, liver, muscle, pituitary, skin, spleen, stomach, and swim bladder) revealed a unique expression pattern in the liver, with the tissue-specific genes exhibiting evolutionary conservation to varying degrees. The highest proportion of core genes was found in the pituitary, whereas the lowest was found in the spleen.

CONCLUSIONS: This study provides comprehensive genomic resources that enhance the understanding of the genetic diversity and evolutionary dynamics of Takifugu species. The findings offer insights for research on both breeding and conservation of Takifugu.},
}

Animals
*Takifugu/genetics/physiology
*Genome
*Genetic Variation
*Animal Migration
Gene Flow

@article {pmid40594904,
year = {2025},
author = {Sayem, M and Rafi, MA and Mishu, ID and Mahmud, Z},
title = {Comprehensive genomic analysis reveals virulence and antibiotic resistance genes in a multidrug-resistant Bacillus cereus isolated from hospital wastewater in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22915},
pmid = {40594904},
issn = {2045-2322},
mesh = {*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects ; *Wastewater/microbiology ; Bangladesh ; *Drug Resistance, Multiple, Bacterial/genetics ; Phylogeny ; Hospitals ; Virulence/genetics ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics/methods ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Humans ; },
abstract = {Hospital wastewater represents a significant reservoir for antimicrobial-resistant bacteria, including multidrug-resistant (MDR) Bacillus cereus, a pathogen of growing concern due to its potential impact on public health and environmental safety. This study characterizes the genomic features, antimicrobial resistance (AMR) mechanisms, and virulence potential of Bacillus cereus MBC, isolated from hospital wastewater in Dhaka, Bangladesh. Using whole-genome sequencing (WGS) and advanced bioinformatics, we analyzed the isolate's taxonomy, phylogenetics, functional annotation, and biosynthetic potential. The genome, spanning 5.6 Mb with a GC content of 34.84%, contained 5,881 protein-coding sequences, including 1,424 hypothetical proteins, and 28 genes associated with AMR. Phylogenetic analysis revealed a close genetic relationship with Bacillus cereus ATCC 14579, sharing virulence factors such as hemolysin BL (HBL), non-hemolytic enterotoxin (NHE), and cytotoxin K (CytK), all contributing to its pathogenicity. The ability to form biofilms further enhances the strain's persistence and resistance in hospital environments. AMR profiling identified genes conferring resistance to beta-lactams (e.g., BcI, BcII, BcIII), tetracyclines (tetB(P)), glycopeptides (vanY), and fosfomycin, highlighting the bacterium's capacity to resist a wide array of antibiotics. Functional annotation revealed metabolic pathways involved in iron acquisition and the biosynthesis of siderophores such as petrobactin and bacillibactin, reinforcing the bacterium's adaptability in nutrient-limited environments. Mobile genetic elements, including prophages, CRISPR-Cas systems, and transposable elements, suggest significant horizontal gene transfer (HGT), enhancing genetic plasticity and resistance spread. Pangenomic analysis, involving 125 B. cereus strains, revealed a high degree of genetic diversity and close relationships with strains from clinical, food, and agricultural environments, emphasizing the overlap between clinical and environmental reservoirs of resistance. The strain's isolation from hospital wastewater underscores the complex interplay between environmental contaminants and bacterial evolution, which fosters MDR traits. Our findings underscore the urgent need for enhanced genomic surveillance and wastewater management strategies to mitigate the spread of MDR B. cereus and AMR genes in hospital environments.},
}

*Bacillus cereus/genetics/pathogenicity/isolation & purification/drug effects
*Wastewater/microbiology
Bangladesh
*Drug Resistance, Multiple, Bacterial/genetics
Phylogeny
Hospitals
Virulence/genetics
Genome, Bacterial
Whole Genome Sequencing
Genomics/methods
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Humans

@article {pmid40594015,
year = {2025},
author = {Zaman, N and Gul, K and Khurram, K and Azam, SS},
title = {Molecular insights into pangenome localization and constructs design for Hemophilus influenza vaccine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22316},
pmid = {40594015},
issn = {2045-2322},
mesh = {Humans ; Molecular Dynamics Simulation ; *Haemophilus influenzae/immunology/genetics ; Bacterial Proteins/immunology/genetics/chemistry ; *Genome, Bacterial ; *Influenza Vaccines/immunology/genetics ; *Influenza, Human/prevention & control/immunology ; Epitopes/immunology/genetics ; },
abstract = {Haemophilus influenza, a major contributor to respiratory infections such as pneumonia, meningitis, sinusitis, chronic bronchitis, and acute otitis, poses a significant public health challenge, driven by rising antibiotic resistance particularly among the non-typeable H. influenza (NTHi) strains given their ability to evade immune surveillance. To address this, we employed a comprehensive immunoinformatics pipeline integrated with extensive pan-genome analysis of 59 strains of H. influenzae to design a novel multiepitope vaccine (MEV) candidate targeting most virulent and clinically significant proteins. Key surface exposed and virulence associated proteins, including Protein E, PilA, Protein D, P4, TolC, YadA, and HifC were prioritized based on their roles in bacterial adhesion, immune evasion, biofilm formation, and nutrient acquisition. Advanced in silico epitope prediction and verification strategies were utilized to map highly immunogenic regions across these proteins, followed by codon optimization to enhance expression efficiency in human systems. To further stabilize the vaccine construct, we performed disulfide engineering to enhance structural integrity and resilience. Comprehensive validation through in silico immune simulations, molecular dynamics (MD) simulations and binding free energy calculations confirmed the structural stability, immunogenic potential, and strong receptor affinity of the MEV candidate. Phylogenetic and virulence factor analysis further corroborated the broad coverage of the pathogenic relevance of the selected proteins. Together, our integrative approach presents a robust pipeline for rational vaccine design, offering a promising avenue toward combating multidrug resistant and immune evasive H. influenza strains.},
}

Humans
Molecular Dynamics Simulation
*Haemophilus influenzae/immunology/genetics
Bacterial Proteins/immunology/genetics/chemistry
*Genome, Bacterial
*Influenza Vaccines/immunology/genetics
*Influenza, Human/prevention & control/immunology
Epitopes/immunology/genetics

@article {pmid40591735,
year = {2025},
author = {Xie, Z and Zheng, H and Cheng, S and Yu, H and Yu, X and Wang, C and Wang, J and Yao, B and Jiang, X and Hu, Y and Jian, A and He, X and Gao, J and Chen, M and Chen, Y and Zhu, Y and Ren, Y and Cheng, Z and Lei, C and Lin, Q and Wang, X and Guo, X and Tian, Y and Liu, S and Liu, X and Jiang, L and Wu, C and Zhu, S and Zhao, Z and Wan, J},
title = {Chromosomal translocations are a significant driver of hybrid sterility in rice.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyaf126},
pmid = {40591735},
issn = {1943-2631},
abstract = {Hybrid sterility is a major barrier in exploiting hybrid vigor in rice grains produced by crossing distantly related parents. While genetic mechanisms such as the killer-protector system have been extensively studied, novel systems underlying hybrid sterility remain poorly characterized. Here, a novel hybrid sterility system governed by two tightly pseudolinked loci SGA1 (on chromosome 1) and SGA2 (on chromosome 2) is reported, which induces semi-sterility in male and female gametes during hybridization between the indica and japonica subspecies. Chromosomal translocations were proposed as the basis for pseudolinkage and unbiased segregation, supported by cytological evidence of meiotic quadrivalent configurations and translocation breakpoint sequences. Gametophytic sterility was identified as the primary driver of dual male-female semi-sterility in translocated heterozygotes. Furthermore, large-segment chromosomal translocations are found to be widespread in rice. Analysis of 120 pangenomic rice accessions revealed that chromosomal translocations are prevalent among cultivars, with one-third exhibiting large translocations (>500-kb). Translocation breakpoints were mainly localized in intergenic and intronic regions, and the disrupted genes were identified as predominantly transposons and retrotransposons. Besides, large translocations were validated through sequence analysis and phenotypic assays. Overall, this study establishes chromosomal translocations as a critical driver of hybrid sterility and provides new insights into heterosis constraints.},
}

@article {pmid40586540,
year = {2025},
author = {Bulka, O and Edwards, EA},
title = {Complete metagenome-assembled genome sequence of Solidesulfovibrio sp. DCME from a dichloromethane dechlorinating microbial community.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0051525},
doi = {10.1128/mra.00515-25},
pmid = {40586540},
issn = {2576-098X},
abstract = {Here, we announce the closed genome of Solidesulfovibrio sp. DCME, assembled from metagenomic sequencing of an anaerobic dichloromethane mineralizing enrichment culture. The Solidesulfovibrio genus is known to cycle hydrogen, a key process for facilitating dichloromethane mineralization, which nominates this microbe as an important player in its microbial community.},
}

@article {pmid40586315,
year = {2025},
author = {Schulman, AH and Hartung, F and Smulders, MJM and Sundström, JF and Wilhelm, R and Rognli, OA and Metzlaff, K},
title = {Proposed EU NGT legislation in light of plant genetic variation.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70228},
pmid = {40586315},
issn = {1467-7652},
support = {210021//Jane ja Aatos Erkon Säätiö/ ; },
abstract = {The European Commission (EC) proposal for New Genomic Techniques (NGTs) of July 2023 specifies that Category 1 NGT (NGT1) plants, which are considered equivalent to conventional plants, that is those obtainable by conventional plant breeding or mutagenesis, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be no more than 20 but of any size. Here, we examine the proposed 20/20 NGT1 limit against the background of the theoretical considerations and older data used to frame it and in light of recent data from highly contiguous long-read assemblies for reference genomes and pangenomes. We find that current genomic data indicate that natural variation in germplasm used by breeders is much greater than earlier understood and that both conventional breeding and mutagenesis can introduce genomic changes that are both more extensive in size and more frequent than the NGT Category 1 '20 insertions of maximum 20 bp' limit would allow. Furthermore, natural variation also scales with genome size and complexity, a factor not considered in the EC proposal. We conclude that the proposed cut-offs under which an NGT plant is considered equivalent to conventional plants do not align with what is observed in nature, conventional breeding and mutagenesis. Updating the 20/20 rule to broader limits would facilitate breeding for climate resilience, farming sustainability and nutritional security, while ensuring that NGT1 plants are equivalent to conventional ones.},
}

@article {pmid40585573,
year = {2025},
author = {Isobe, S},
title = {Unlocking the potential of genetic resources in the Pangenome era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {1},
pmid = {40585573},
issn = {1344-7610},
}

@article {pmid40585572,
year = {2025},
author = {Sato, K},
title = {Genetic resources and pangenome analysis of barley.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {13-20},
pmid = {40585572},
issn = {1344-7610},
abstract = {Barley (Hordeum vulgare) is widely cultivated, ranking fourth in cultivation area among cereal crops worldwide. Many wild and cultivated barley accessions have been collected and preserved in crop genebanks throughout the world. Barley has a large genome (~5 Gbp) that has recently been sequenced and assembled at the chromosome level by the international research community. The community also is sequencing accessions representing the diversity of both domesticated and wild barley to provide genome-wide genotyping information for pangenome analysis. Given that the pangenome represents the universe of genome sequences existing in a species, the long-term goal of this project is to obtain high-quality genome sequences of the major barley accessions worldwide. As each accession is annotated, the capacity to explore structural differences is enhanced by the increased understanding of the diversity of the barley genome, which will facilitate efficient development of cultivars for human consumption. This review describes our current knowledge of barley genome diversity and proposes future directions for basic and applied research of the barley pangenome.},
}

@article {pmid40585571,
year = {2025},
author = {Aoyagi Blue, Y and Iimura, H and Sato, MP and Shirasawa, K},
title = {The impact of telomere-to-telomere genome assembly in the plant pan-genomics era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {3-12},
pmid = {40585571},
issn = {1344-7610},
abstract = {Advances in sequencing technologies have enabled the determination of genome sequences of multiple lines within a single species. Comparative analysis of multiple genome sequences reveals all genes present within a species, providing insight into the genetic mechanisms that lead to the establishment of species. Highly accurate pan-genome analysis requires telomere-to-telomere gapless genome assembly, providing an ultimate genome sequence that covers all chromosomal regions without any undetermined nucleotide sequences. This review describes the genome sequencing technologies and sophisticated bioinformatics required for telomere-to-telomere gapless genome assembly, as well as a genetic mapping that can evaluate the accuracy of telomere-to-telomere genome assembly. Pan-genome analyses may contribute to the understanding of genetic mechanisms not only within a single species but also across species.},
}

@article {pmid40585570,
year = {2025},
author = {Shigita, G and Tanaka, K and Kato, K},
title = {Current and future pangenomic research in cucurbit crops.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {34-50},
doi = {10.1270/jsbbs.24048},
pmid = {40585570},
issn = {1344-7610},
abstract = {Pangenomics is the exploration and characterization of the full spectrum of genetic variation within a species or a given taxonomic clade. Driven by the accelerating decline in sequencing costs and the widespread adoption of long-read sequencing technologies, the "wave" of pangenomics is now hitting various major crops, uncovering substantial intraspecific diversity previously underestimated and neglected. This includes crops belonging to the gourd family (Cucurbitaceae), such as cucumber (Cucumis sativus), melon (Cucumis melo), watermelon (Citrullus lanatus), wax gourd (Benincasa hispida), and bottle gourd (Lagenaria siceraria), all of which are important on a global or regional scale. In this review, we consolidate the findings from all nine pangenomic studies reported as of June 2024, on the five cucurbit crops listed above. This summarizes the current state of pangenomics in the family. We then highlight remaining knowledge gaps for each crop, and propose further research to fill these gaps. Finally, we discuss how pangenomics will shape the future of crop breeding and expand the framework of crop genetic resources in synergy with other technological advances. These insights would apply not only to cucurbits but also to crops across diverse families.},
}

@article {pmid40585569,
year = {2025},
author = {Yoshikawa, T and Sato, Y},
title = {Usage of wild Oryza germplasms for breeding in pan-genomics era.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {51-60},
doi = {10.1270/jsbbs.24050},
pmid = {40585569},
issn = {1344-7610},
abstract = {One approach to sustainable agricultural production in a changing global environment is the effective utilization of unutilized germplasms. Among these, crop wild relatives (CWRs) represent valuable germplasms that retain the diversity lost during domestication. The genus Oryza has two cultivated species and 22 wild species. One of the cultivated species, Oryza sativa, produces the rice that is the staple food for half of the world's population. We are responsible for the maintenance and distribution of wild Oryza genetic resources held by Japan's National Institute of Genetics (NIG). The NIG has collected the genome sequences of numerous wild Oryza accessions, aiming at understanding and promoting the utilization of Oryza germplasm for both basic and applied sciences, such as breeding. The genome information of many wild Oryza germplasms deciphered by multiple groups is publicly available in databases, allowing for pangenome analysis. This review mainly introduces the wild Oryza genetic resources held by the NIG, discusses the genome diversity revealed through genome sequencing, presents new attempts to utilize wild Oryza germplasm as novel resources enabled by genome sequencing, and discusses the challenges in further effectively utilizing wild Oryza germplasm in breeding.},
}

@article {pmid40585568,
year = {2025},
author = {Chapman, MA},
title = {Novel breeding resources for the underutilised legume, lablab, based on a pangenome approach.},
journal = {Breeding science},
volume = {75},
number = {1},
pages = {61-66},
doi = {10.1270/jsbbs.24055},
pmid = {40585568},
issn = {1344-7610},
abstract = {Individuals across a species exhibit substantial presence-absence variation, to the extent that a reference genome from a single individual only contains a subset of the species' genome. Cataloguing genome regions absent from a reference genome can therefore reveal novel genome regions, and some of this variation can be adaptive. In this work, existing short sequencing reads for the underutilised crop lablab (Lablab purpureus (L.) Sweet) were used to identify regions of the genome absent from the reference genome. Lablab is made up of two distinct gene pools, each with wild and domesticated types therefore represents an opportunity to identify gene pool-specific variation. Approximately 7.7% of the reads from eight accessions failed to map to the lablab reference genome (cv. Highworth), putatively being novel, and these were assembled and collapsed into between 735 and 12,304 contigs. Four samples were focussed on (one each wild and domesticated from each of the gene pools) and the novel contigs compared, to identify those present only in subsets of samples. Whilst the number of contigs containing sequenced with similarity to known genes in other legumes was low, there were some enriched gene ontology (GO) terms that could relate to adaptive differences between the groups and therefore contain novel genes for future lablab breeding. The approached used here has potential use in any other species.},
}

@article {pmid40579690,
year = {2025},
author = {Huang, G and Li, L and Cao, X and Lin, H},
title = {Alfalfa pan-genome unveiled-a breakthrough in alfalfa genomics-assisted breeding.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40579690},
issn = {1869-1889},
}

@article {pmid40577690,
year = {2025},
author = {Tanaka, T and Haraguchi, Y and Todoroki, T and Saisho, D and Abiko, T and Kai, H},
title = {Reference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf016},
pmid = {40577690},
issn = {1756-1663},
abstract = {Current advances in next generation sequencing (NGS) technology and assembling programs permits construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex.' We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B and D homoeologs, respectively), and rice. From the GO analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as "response to biotic and abiotic stress" and "metabolic process". Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.},
}

@article {pmid40573859,
year = {2025},
author = {Zhang, W and Zhou, L and Ni, D and Ni, J and Song, F and Yang, L and Zhang, D},
title = {Genetic Analysis of Lodging Resistance in 1892S Based on the T2T Genome: Providing a Genetic Approach for the Improvement of Two-Line Hybrid Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {40573859},
issn = {2223-7747},
support = {U21A20211//National Natural Science Foundation of China/ ; },
abstract = {Successfully breeding high-yield, lodging-resistant hybrid rice varieties is critical for ensuring food security. Two-line hybrid rice system plays an essential role in rice breeding, and 1892S, an important two-line sterile line, has contributed significantly to the development of over 100 hybrid rice varieties with superior agronomic traits, including lodging resistance. Despite its importance, a comprehensive understanding of the genomic basis underlying these traits in 1892S has been lacking due to the limitations of short-read sequencing technologies. To address this gap, we utilized advanced telomere-to-telomere (T2T) genome assembly techniques to generate a high-quality, gap-free genome of 1892S-the final genome comprises 12 complete chromosomes with 40,560 protein-coding genes. Comparative genomic analysis identified multiple known lodging resistance genes, including SD1, Sdt97, SBI, OsFBA2, APO1, and OsTB1, with unique allelic variations that may enhance resistance. The pan-genome analysis identified 2347 strain-specific genes in 1892S, further supporting its unique genetic advantages. This study represents the complete T2T genome assembly of a two-line sterile line and provides novel insights into the genetic foundation of lodging resistance in hybrid rice. This study highlights the genetic potential of 1892S in hybrid rice breeding and provides a model for the genomic analysis of other two-line sterile lines, offering valuable insights for improving in hybrid rice, including traits lodging resistance, yield stability, and adaptability, which are crucial for global food security.},
}

@article {pmid40572210,
year = {2025},
author = {Wang, Y and Hao, J and Gu, J and Wu, J and Zhang, Y and Liang, T and Bai, H and Cao, Q and Jiang, J and Li, L and Cao, X},
title = {Genome-Driven Functional Validation of Bacillus amyloliquefaciens Strain MEPW12: A Multifunctional Endophyte for Sustainable Sweet Potato Cultivation.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572210},
issn = {2076-2607},
support = {32471584//National Natural Science Foundation of China/ ; 32030072//National Natural Science Foundation of China/ ; KYCX22_2814//Postgraduate Research and Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Sweet potato (Ipomoea batatas (L.) Lam.), as an important crop, is rich in polyphenols, vitamins, minerals, and other nutrients in its roots and leaves and is gradually gaining popularity. The use of endophytic bacteria to improve the quality of sweet potato can protect the environment and effectively promote the sustainable development of the sweet potato industry. In this study, 12 strains of endophytic bacteria were isolated from sweet potato. Through nitrogen fixation, phosphorus solubilization, indoleacetic acid production, siderophore production, ACC deaminase production, and carboxymethyl cellulose production, three strains with multiple biological activities were screened out. Among them, MEPW12 had the most plant growth-promoting functions. In addition, MEPW12 promoted host chlorophyll accumulation and inhibited pathogen growth and colonization in sweet potato roots and can utilize various carbon sources and salts for growth. It can also grow in extreme environments of high salt and weak acid. MEPW12 was identified as Bacillus amyloliquefaciens with a genome size of 3,928,046 bp and a GC content of 46.59%. After the annotation of multiple databases, it was found that MEPW12 had multiple enzymatic activities and metabolic potential. Comparative genomics and pan-genomics analyses revealed that other Bacillus sp. strains of MEPW12 have similar functions. However, due to adaptation to different growth environments, there are still genomic differences and changes. Inoculation with MEPW12 induced the high expression of IbGH3.10, IbERF1, and other genes, thereby promoting the growth of sweet potatoes. Bacillus amyloliquefaciens strain MEPW12 is a sweet potato endophyte with multiple growth-promoting functions, which can promote the growth of sweet potato seedlings. This study provides new microbial resources for developing microbial agents and improving the quality of sweet potatoes.},
}

@article {pmid40572063,
year = {2025},
author = {Shi, J and Su, H and He, S and Dai, S and Mao, H and Wu, D},
title = {Pan-Genomic Insights into Rumen Microbiome-Mediated Short-Chain Fatty Acid Production and Regulation in Ruminants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572063},
issn = {2076-2607},
abstract = {The rumen microbiome represents a cornerstone of ruminant digestive physiology, orchestrating the anaerobic fermentation of plant biomass into short-chain fatty acids (SCFAs)-critical metabolites underpinning host energy metabolism, immune function, and environmental sustainability. This comprehensive review evaluates the transformative role of pan-genomics in deciphering the genetic and metabolic networks governing SCFA production in the rumen ecosystem. By integrating multi-omics datasets, pan-genomic approaches unveil unprecedented layers of microbial diversity, enabling precise identification of core functional genes and their dynamic contributions to carbohydrate degradation and SCFA biosynthesis. Notable advancements include the following: mechanistic insights into microbial community assembly and metabolic pathway regulation, highlighting strain-specific adaptations to dietary shifts; precision interventions for optimizing feed efficiency, such as rationally designing microbial consortia and screening novel feed additives through pan-genome association studies; and sustainability breakthroughs, demonstrating how targeted modulation of rumen fermentation can simultaneously enhance production efficiency and mitigate methane emissions. This synthesis underscores the potential of pan-genomics to revolutionize ruminant nutrition, offering a blueprint for developing next-generation strategies that reconcile agricultural productivity with environmental stewardship. The translational applications discussed herein position pan-genomics as a critical tool for advancing animal science and fostering a resilient livestock industry.},
}

@article {pmid40567591,
year = {2025},
author = {Rozanova, IV and Vodiasova, EA},
title = {Modern methods in peach (Prunus persica) genome research.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {29},
number = {3},
pages = {358-369},
doi = {10.18699/vjgb-25-39},
pmid = {40567591},
issn = {2500-0462},
abstract = {Peach (Prunus persica (L.) Batsch) is one of the main agricultural stone fruit crops of the family Rosaceae. Modern breeding is aimed at improving the quality of the fruit, extending the period of its production, increasing its resistance to unfavorable environmental conditions and reducing the total cost of production of cultivated varieties. However, peach breeding is an extremely long process: it takes 10-15 years from hybridization of the parental forms to obtaining fruit-bearing trees. Research into peach varieties as donors of desirable traits began in the 1980s. The first version of the peach genome was presented in 2013, and its appearance contributed to the identification and localization of loci, followed by the identification of candidate genes that control the desired trait. The development of NGS has accelerated the development of methods based on the use of diagnostic DNA markers. Approaches that allow accelerating classical breeding processes include marker-oriented selection (MOS) and genomic selection. In order to develop DNA markers associated with the traits under investigation, it is necessary to carry out preliminary mapping of loci controlling economically desirable traits and to develop linkage maps. SNP-chip approaches and genotyping by sequencing (GBS) methods are being developed. In recent years, genome-wide association analysis (GWAS) has been actively used to identify genomic loci associated with economically important traits, which requires screening of large samples of varieties for hundreds and thousands of SNPs. Study on the pangenome has shown the need to analyze a larger number of samples, since there is still not enough data to identify polymorphic regions of the genome. The aim of this review was to systematize and summarize the major advances in peach genomic research over the last 40 years: linkage and physical map construction, development of different molecular markers, full genome sequencing for peach, and existing methods for genome-wide association studies with high-density SNP markers. This review provides a theoretical basis for future GWAS analysis in order to identify high-performance markers of economically valuable traits for peach and to develop genomic selection of this crop.},
}

@article {pmid40565594,
year = {2025},
author = {Saccone, S and Brancato, D and Bruno, F and Coniglio, E and Sturiale, V and Federico, C},
title = {Origin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
pmid = {40565594},
issn = {2073-4425},
mesh = {Humans ; *Evolution, Molecular ; Animals ; *Eukaryota/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Selection, Genetic ; },
abstract = {The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.},
}

Humans
*Evolution, Molecular
Animals
*Eukaryota/genetics
Gene Duplication
Gene Transfer, Horizontal
Selection, Genetic

@article {pmid40560760,
year = {2025},
author = {Sia, CM and Ambrose, RL and Valcanis, M and Andersson, P and Ballard, SA and Howden, BP and Williamson, DA and Pearson, JS and Ingle, DJ},
title = {Distinct adaptation and epidemiological success of different genotypes within Salmonella enterica serovar Dublin.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40560760},
issn = {2050-084X},
support = {GNT1174555//National Health and Medical Research Council/ ; SMRF22008//Sylvia and Charles Viertel Charitable Foundation/ ; GNT1196103//National Health and Medical Research Council/ ; GNT1195210//National Health and Medical Research Council/ ; Medical Research Future Fund FSPGN000045//Australian Government/ ; },
mesh = {*Salmonella enterica/genetics/drug effects/pathogenicity/classification ; Humans ; *Salmonella Infections/microbiology/epidemiology ; *Genotype ; Virulence ; Plasmids/genetics ; Genome, Bacterial ; Serogroup ; Phylogeny ; Australia/epidemiology ; Genomic Islands ; Drug Resistance, Bacterial ; *Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Salmonella Dublin is a host-adapted, invasive nontyphoidal Salmonella (iNTS) serovar that causes bloodstream infections in humans and demonstrates increasing prevalence of antimicrobial resistance (AMR). Using a global dataset of 1303 genomes, coupled with in vitro assays, we examined the evolutionary, resistance, and virulence characteristics of S. Dublin. Our analysis revealed strong geographical associations between AMR profiles and plasmid types, with highly resistant isolates confined predominantly to North America, linked to IncC plasmids co-encoding AMR and heavy metal resistance. By contrast, Australian isolates were largely antimicrobial-susceptible, reflecting differing AMR pressures. We identified two phylogenetically distinct Australian lineages, ST10 and ST74, with a small number of ST10 isolates harbouring a novel hybrid plasmid encoding both AMR and mercuric resistance. Whereas the ST10 lineage remains globally dominant, the ST74 lineage was less prevalent. ST74 exhibited unique genomic features including a larger pan genome compared to ST10 and the absence of key virulence loci, including Salmonella pathogenicity island (SPI)-19 which encodes a type VI secretion system (T6SS). Despite these genomic differences, the ST74 lineage displayed enhanced intracellular replication in human macrophages and induced less pro-inflammatory responses compared with ST10, suggesting alternative virulence strategies that may support systemic dissemination of ST74. The Vi antigen was absent in all ST10 and ST74 genomes, highlighting challenges for serotyping and vaccine development, and has implications for current diagnostic and control strategies for S. Dublin infections. Collectively, this study represents the most comprehensive investigation of S. Dublin to date and, importantly, has revealed distinct adaptations of two genotypes within the same serovar, leading to different epidemiological success. The regional emergence and evolution of distinct S. Dublin lineages highlight the need to understand the divergence of intra-serovar virulence mechanisms which may impact the development of effective control measures against this important global pathogen.},
}

*Salmonella enterica/genetics/drug effects/pathogenicity/classification
Humans
*Salmonella Infections/microbiology/epidemiology
*Genotype
Virulence
Plasmids/genetics
Genome, Bacterial
Serogroup
Phylogeny
Australia/epidemiology
Genomic Islands
Drug Resistance, Bacterial
*Adaptation, Physiological
Anti-Bacterial Agents/pharmacology

@article {pmid40559531,
year = {2025},
author = {Ajmi, N and Duman, M and Ay, H and Saticioglu, IB},
title = {Genomic and Pangenomic Insights into Aeromonas salmonicida subsp. oncorhynchi subsp. nov.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559531},
issn = {2076-0817},
support = {TGA-2024-1797//Research Fund of Bursa Uludag University/ ; },
mesh = {*Aeromonas salmonicida/genetics/classification/isolation & purification/pathogenicity ; Animals ; Phylogeny ; *Genome, Bacterial ; Virulence Factors/genetics ; *Oncorhynchus mykiss/microbiology ; Genomics ; *Fish Diseases/microbiology ; *Gram-Negative Bacterial Infections/microbiology/veterinary ; Whole Genome Sequencing ; Plasmids/genetics ; },
abstract = {The strain A-9[T], isolated from Oncorhynchus mykiss (rainbow trout) in a Turkish aquaculture facility, was characterized through integrated phenotypic, phylogenetic, and genomic analyses. Whole-genome sequencing revealed a 5.21 Mb circular chromosome (GC content: 58.16%) and three plasmids encoding proteins for mobilization and toxin-antitoxin systems. Multilocus phylogenetic analysis (MLPA) using seven housekeeping genes supported the distinct lineage of A-9[T]. Digital DNA-DNA hybridization (77.6-78.6%) and average nucleotide identity values (96.59-97.58%) confirmed taxonomic divergence from all currently recognized A. salmonicida subspecies. Comparative proteomic and pangenomic analyses identified 328 strain-specific genes, including virulence factors, secretion system components (Type II and Type VI), and efflux-related proteins. Although genes encoding Type III secretion systems and biofilm formation were absent, A-9[T] harbored a broad virulence gene repertoire and resistance determinants, including OXA-956, cphA5, and FOX-20, supporting a multidrug-resistant phenotype. Based on its genomic, phenotypic, and functional distinctiveness, we propose the novel taxon Aeromonas salmonicida subsp. oncorhynchi subsp. nov. (type strain A-9[T] = LMG 33538[T] = DSM 117494[T]), expanding the taxonomic landscape of the A. salmonicida complex and offering insights into fish-associated bacterial evolution.},
}

*Aeromonas salmonicida/genetics/classification/isolation & purification/pathogenicity
Animals
Phylogeny
*Genome, Bacterial
Virulence Factors/genetics
*Oncorhynchus mykiss/microbiology
Genomics
*Fish Diseases/microbiology
*Gram-Negative Bacterial Infections/microbiology/veterinary
Whole Genome Sequencing
Plasmids/genetics

@article {pmid40558202,
year = {2025},
author = {Chaichana, N and Suwannasin, S and Boonsan, J and Yaikhan, T and Klaysubun, C and Singkhamanan, K and Wonglapsuwan, M and Pomwised, R and Konglue, S and Chema, R and Saivaew, M and Surachat, K},
title = {Genomic Characterization and Safety Evaluation of Enterococcus lactis RB10 Isolated from Goat Feces.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40558202},
issn = {2079-6382},
abstract = {Background: The genus Enterococcus includes a diverse group of bacteria that are commonly found in the gastrointestinal tracts of humans and animals, as well as in various environmental habitats. Methods: In this study, Enterococcus lactis RB10, isolated from goat feces, was subjected to comprehensive genomic and functional analysis to assess its safety and potential as a probiotic strain. Results: The genome of E. lactis RB10, with a size of 2,713,772 bp and a GC content of 38.3%, was assembled using Oxford Nanopore Technologies (ONT). Genome annotation revealed 3375 coding sequences (CDSs) and highlighted key metabolic pathways involved in carbohydrate, protein, and amino acid metabolism. The strain was susceptible to important antibiotics, including ampicillin, chloramphenicol, tetracycline, and vancomycin, but exhibited resistance to aminoglycosides, a common trait in Enterococcus species with non-hemolytic activity. Genomic analysis further identified two intrinsic antimicrobial resistance genes (ARGs). The strain also demonstrated antimicrobial activity against Bacillus cereus DMST 11098 and Salmonella Typhi DMST 22842, indicating pathogen-specific effects. Key genes for adhesion, biofilm formation, and stress tolerance were also identified, suggesting that RB10 could potentially colonize the gut and compete with pathogens. Moreover, the presence of bacteriocin and secondary metabolite biosynthetic gene clusters suggests its potential for further evaluation as a biocontrol agent and gut health promoter. Conclusions: However, it is important to note that E. lactis RB10 was isolated from goat feces, a source that may harbor both commensal and opportunistic bacteria, and therefore additional safety assessments are necessary. While further validation is needed, E. lactis RB10 exhibits promising probiotic properties with low pathogenic risk, supporting its potential use in food and health applications.},
}

@article {pmid40556891,
year = {2025},
author = {Chekole, WS and Potgieter, L and Adamu, H and Sternberg-Lewerin, S and Tessema, TS and Magnusson, U},
title = {Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597580},
pmid = {40556891},
issn = {1664-302X},
abstract = {Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI ≥ 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n ≥ 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.},
}

@article {pmid40554012,
year = {2025},
author = {Qi, Y and Patel, MH and Lu, SY and Skory, CD},
title = {Genomic insights into persistence, antibiotic resistance, and intraspecific diversity of lactic acid bacterial contaminants at corn dry-grind fuel ethanol facilities.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132836},
doi = {10.1016/j.biortech.2025.132836},
pmid = {40554012},
issn = {1873-2976},
abstract = {During fuel ethanol production, fermenter tanks are persistently contaminated by lactic acid bacteria (LAB), lowering ethanol yields and causing costly shutdowns for cleaning. In this study, whole-genome sequencing was conducted for 156 Lactiplantibacillus plantarum, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus mucosae isolates previously obtained in a two-year longitudinal study at a U.S. Midwest corn dry-grind fuel ethanol production facility. Striking similarity between genomes for isolates collected during different years reveal the strong ability of LAB strains to persist in bioethanol fermentation facilities. Furthermore, comparison of bioethanol contaminant genomes and previously published genomes in the same species from other environments showed a smaller, closed pangenome for bioethanol contaminants, indicating their specialization for this niche. Additionally, 39 genomes contained a putative plasmid or transposable element encoding for resistance to the antibiotic virginiamycin, frequently used by fermentation facilities to control LAB contamination. Finally, comparison of L. fermentum isolates that strongly inhibited Saccharomyces cerevisiae fermentation and less inhibitory isolates suggest there may be genetic and metabolic changes underlying these differences. To our knowledge, this study represents the first large-scale genomic analysis for LAB contaminants of bioethanol production, providing new insights into the biology of industrial microbial contaminants that have enormous economic impact.},
}

@article {pmid40553877,
year = {2025},
author = {Saleem, S and Amin, W and Bhatti, F and Majid, M and Fazal, A},
title = {Nucleic acid-based strategies to mitigate stripe rust disease of wheat for achieving global food security - A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145353},
doi = {10.1016/j.ijbiomac.2025.145353},
pmid = {40553877},
issn = {1879-0003},
abstract = {Wheat (Triticum aestivum), being a global staple crop, is critical in ensuring food security due to its significant nutritional value. However, it faces numerous challenges from both biotic and abiotic stresses, with fungal diseases being particularly detrimental to yield. Among these, wheat stripe rust, caused by the fungal pathogen Puccinia striiformis, poses a severe threat to wheat. Globally, 5.47 million tons of grains are lost due to the stripe rust pathogen, equivalent to a loss of USD 979 million annually; almost 88 % of the world's wheat production is susceptible to stripe rust. This review accentuates the global extensive distribution of stripe rust, detailing its causes and impact on crop productivity and mitigating approaches following traditional, genomic, and post-genomics. The mitigation approaches to wheat stripe rust have been mainly categorized into primitive (pre-genomic), modern (genomic), and next-generation (post-genomic) approaches. The primitive approaches include traditional breeding, phenotypic selection, and exotic germplasm to introduce resistance leads to early success in disease management. The advanced genomic era, with tools like QTL mapping, GWAS, marker-assisted selection, and high-throughput sequencing to deploy resistance genes, helps in precise mapping and developing high-throughput genotyping for large-scale screening and introgression of multiple resistant genes. The gene-editing approaches, including CRISPR/Cas9, RNAi, and epigenomics, now enable precise gene editing and regulation for durable resistance, together with multi-omics techniques, to identify resistant pathways and biomarkers with enhanced understanding of host-pathogen interactions and resistance mechanisms. Climate change events like shifts in rainfall patterns and rising temperatures expand the rust-prone area and pose more challenges in developing durable rust-resistant cultivars. Furthermore, the review explores using wheat's valuable genetic resources and integrating AI-based technologies to enhance stripe rust resistance by analyzing large datasets, including pathogen evolution and growth stages, allowing for timely interventions of the stripe rust epidemic. The role of multiomics approaches, particularly genomics and transcriptomics, in unraveling the genetic basis of stress tolerance is highlighted. A forward-looking framework is proposed, emphasizing the use of interdisciplinary methodologies, including big data, multi-omics, and AI-driven approaches, that hold immense promise to revolutionize wheat protection with the development of climate-resilient wheat genotypes and ensure real-time disease monitoring and precision-resistant strategies against the evolving rust pathogen.},
}

@article {pmid40553094,
year = {2025},
author = {Dobhal, S and Hugouvieux-Cotte-Pattat, N and Arizala, D and Sari, GB and Chuang, SC and Alvarez, AM and Arif, M},
title = {Dickeya ananatis sp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus).},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006822},
pmid = {40553094},
issn = {1466-5034},
mesh = {*Ananas/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Nucleic Acid Hybridization ; Bacterial Typing Techniques ; Genome, Bacterial ; Sequence Analysis, DNA ; *Dickeya/classification/genetics/isolation & purification ; Multilocus Sequence Typing ; Hawaii ; Malaysia ; Plant Diseases/microbiology ; },
abstract = {Species clustering within Dickeya zeae has been recently identified as complex, encompassing validly published names, including Dickeya oryzae and Dickeya parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93 to 99.9% and 91.8 to 99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae and D. oryzae ranged from 94.4-95.9% to 57.2-66.5%, respectively. These values fall below the proposed boundaries for species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis of ten housekeeping genes, whole genome and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the 7 pineapple strains. Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological and phylogenomic analyses, we propose the reclassification into a new species of the five pineapple strains from Hawaii A5391, A5410[T], A5611, A6136 and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananatis sp. nov. for this taxon, represented by the type strain A5410[T] (=ICMP 25020[T]=LMG 33197[T]).},
}

*Ananas/microbiology
*Phylogeny
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Nucleic Acid Hybridization
Bacterial Typing Techniques
Genome, Bacterial
Sequence Analysis, DNA
*Dickeya/classification/genetics/isolation & purification
Multilocus Sequence Typing
Hawaii
Malaysia
Plant Diseases/microbiology

@article {pmid40552806,
year = {2025},
author = {Beebe, MA and Paredes-Sabja, D and Kociolek, LK and Rodríguez, C and Sorg, JA},
title = {Phenotypic analysis of various Clostridioides difficile ribotypes reveals consistency among core processes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0096425},
doi = {10.1128/aem.00964-25},
pmid = {40552806},
issn = {1098-5336},
abstract = {Clostridioides difficile infections (CDI) cause almost 300,000 hospitalizations per year, of which ~15%-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings have resulted in an extensive collection of C. difficile clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent epidemic ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and/or increased recurrence rates, but why certain ribotypes are more prominent or harmful than others remains unknown. Because C. difficile has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of C. difficile. Thus, we hypothesize that the core biological processes of C. difficile are conserved across ribotypes/clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, production of toxin A and toxin B, bile acid sensitivity, bile salt hydrolase activity, and surface motility of 15 strains belonging to various ribotypes spanning each known C. difficile clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades/ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host factors.IMPORTANCEClostridioides difficile infections impact thousands of individuals every year, many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades/ribotypes of C. difficile and disease severity/recurrence. Here, we demonstrate that C. difficile strains across major clades/ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity/recurrence and are ideal targets for the development of therapeutics meant to treat C. difficile-related infections.},
}

@article {pmid40552804,
year = {2025},
author = {Eichelman, MC and Meyer, MM},
title = {Assessing the conservation and targets of putative sRNAs in Streptococcus pneumoniae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0325224},
doi = {10.1128/spectrum.03252-24},
pmid = {40552804},
issn = {2165-0497},
abstract = {UNLABELLED: RNA regulators are often found in regulatory networks and mediate growth and virulence in bacteria. Small RNAs (sRNAs) are non-coding RNAs that modulate translation initiation and mRNA degradation by base pairing. To better understand the role of sRNAs in pathogenicity, several studies identified sRNAs in Streptococcus pneumoniae; however, little functional characterization has followed. This study's goals are to (i) survey putative sRNAs in S. pneumoniae; (ii) assess the conservation of these sRNAs; and (iii) examine their predicted targets. Three previous studies in S. pneumoniae identified 287 putative sRNAs by high-throughput sequencing. This study narrows the candidates down to 58 putative sRNAs. BLAST analysis indicates that the 58 sequences are highly conserved across the S. pneumoniae pangenome, and 25 are identified sporadically in other Streptococcus species. However, only two have corresponding sequences identified across several Streptococcus species. We used four RNA-target prediction programs to predict targets for each of the 58 putative sRNAs. Across all probable predictions, six sRNAs have overlapping targets predicted by multiple programs, four targeting numerous transposase-encoding transcripts. sRNAs targeting transposase-encoding transcripts display nearly identical and perfect base pairing. One sRNA, M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in carbon metabolism control. Each M63-target interaction exhibits unique base pairing, increasing confidence in the biological relevance of the result. This study produces a list of S. pneumoniae putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.

IMPORTANCE: Previous studies identified many small RNA candidates in Streptococcus pneumoniae, several of which were hypothesized to play a role in S. pneumoniae virulence. Due to the differing sequencing methods, diverse inclusion criteria, S. pneumoniae strain differences, as well as limited follow-up, it is unclear to what extent candidates identified in different studies have overlapping sequences and functions, and their biological relevance remains ambiguous. This research aims to consolidate the candidate sRNAs across these studies and focuses attention on those that are likely to be regulatory and associated with virulence. This study's findings enhance our knowledge of the conservation of small regulatory RNAs across the many Streptococcus pneumoniae strains and highlight a handful that appear likely to have a role in growth or virulence.},
}

@article {pmid40549295,
year = {2025},
author = {Bhat, T and Kumar, M and Ballamoole, KK and Deekshit, VK and Gollapalli, P},
title = {Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40549295},
issn = {1573-501X},
abstract = {The increasing prevalence of Acinetobacter baumannii infections and its severity demand the acute necessity for innovative therapeutic targets against it. This study employs comprehensive pangenome analysis to investigate 124 A. baumannii multidrug-resistant strains, to determine the most promising therapeutic targets derived from its core genome. Nucleotide diversity analysis of core and variable gene clusters identified key polymorphisms, suggesting significant evolutionary adaptation. Our findings revealed significant presence/absence variation (PAV) in resistance genes across strains, with 97 antimicrobial drug resistance genes identified. Two gene clusters, cluster-288 and cluster-566, harbored resistance-related genes encoding for beta-lactamase and multidrug efflux pump, respectively, were identified from the core genome that plays a pivotal role in conferring multidrug resistance. The functional enrichment analysis of these gene clusters highlighted key proteins, such as penicillin-binding proteins and outer membrane efflux proteins, as potential targets for drug design. Furthermore, we analyzed the physicochemical properties, virulence potential, active site prediction, and predicted conserved motifs. Structural predictions via 3D modeling and molecular dynamics simulations revealed high stability of key proteins, with RMSD values of 0.52 nm for outer membrane channel subunit AdeK and 0.85 nm for beta-lactamase, suggesting these proteins' potential as novel drug targets and their structural integrity under physiological conditions. Principal component analysis (PCA) highlighted distinct motion patterns within these proteins, providing insights into their functional dynamics. This research contributes to ongoing efforts to combat antibiotic resistance through innovative approaches in drug design and therapeutic interventions.},
}

@article {pmid40545607,
year = {2025},
author = {Yu, Z and Lei, T and Yi, X and Hao, Y and Wu, S and Xiao, Z and Qu, J and Li, S and Wang, L and Li, Y and Zhang, L and Pan, Y and Wang, Y and Gou, L and Jiao, Y and Wang, J},
title = {LGRPv2: A high-value platform for the advancement of Fabaceae genomics.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70220},
pmid = {40545607},
issn = {1467-7652},
support = {32470676//National Natural Science Foundation of China/ ; 32170236//National Natural Science Foundation of China/ ; 31501333//National Natural Science Foundation of China/ ; C2020209064//Hebei Natural Science Foundation/ ; C2024209014//Hebei Natural Science Foundation/ ; H2023209084//Hebei Natural Science Foundation/ ; 246Z2508G//Central Guiding Local Science and Technology Development Fund Project/ ; ZD-YG-202313-23//Key Research Project of North China University of Science and Technology/ ; },
abstract = {Fabaceae, as one of the most diverse angiosperm families, plays a crucial role in maintaining global ecosystems and advancing human civilization. With the rapid accumulation of legume genomes, we developed LGRPv2 (https://fabaceae.cgrpoee.top), an updated version of the Legume Genomics Research Platform. LGRPv2 integrates 413 genomes, covering all published legume genomes and containing our latest deciphered Tamarindus indica genome from early-diverging legumes and three outgroup genomes (Euscaphis pleiosperma, Vitis vinifera, and Platycodon tenuifolia). It features user-friendly interactive interfaces for studying functional annotations, gene duplications, regulatory proteins, N[6]-methyladenosine modifications, and transposable elements. For easily exploring genome evolution associated with polyploidizations, we incorporated DotView, SynView, and DecoBrowse with genome synteny (GenS) to establish a central GenS database for legumes. Specialized web services for ancestral legume genomes enable scientists to analyse the role of paleogenome reshuffling in shaping genomic diversity. The platform offers 184 511 synteny-based orthogroups and 1 086 836 genes from 139 families, and tools to explore agronomic trait origins. LGRPv2 integrates 40 550 transcriptomes, 5091 pan-genomes, 12 136 metabolomes, species encyclopaedias, ecological resources, and literature for exploring legume genomics comprehensively. Furthermore, LGRPv2 implemented 58 window-based operating tools (31 new) to efficiently support new mining, especially in advancing assembling pipelines for polyploidization identification, ancestral genome reconstruction, and gene family evolution. Finally, we provided detailed usage guides and community support to empower LGRPv2 with user-friendly and continuously updated features.},
}