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3689 results

Full text 2025

Genetic and virulence factors behind the success of high-risk <i>Pseudomonas aeruginosa</i> clones: insights from comparative genomics and an experimental infection model

de Sales RO, Leaden L, Martins DS, et al.

<h4>Introduction</h4><i>Pseudomonas aeruginosa</i> causes severe healthcare-associated infections. High-risk clones are defined by global dissemination and multidrug resistance, yet virulence is heterogeneous. We sought to map accessory-genome determinants associated with high-risk clones by integrating whole-genome sequencing (WGS) …

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Bioinformatics

Full text 2026

Emergence of Candida (Candidozyma) auris in Minas Gerais, Brazil: Genomic Surveillance to Guide Rapid Public Health Responses

Tomé LMR, Camargo DRA, Bastos RW, et al.

<h4>Background</h4>Candida (Candidozyma) auris is an emerging yeast that poses a significant global health threat due to its multidrug resistance and ability to cause healthcare-associated outbreaks. Genomic surveillance is essential for monitoring spread, transmission and antifungal …

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Bioinformatics

Full text 2024

Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

Wen J, Zhu JW, Ma XD, et al.

<h4>Background</h4>Tribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, the genomic information of these group species has not been widely developed, …

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Bioinformatics

Full text 2025

An Integrated Study of Ramie (<i>Boehmeria nivea</i>), and Its Wild, Cultivated, and Feral Forms

Zhao Y, Milne RI, Liu J, et al.

Feralization, the re-establishment of wild populations from domesticated ancestors, can involve multiple parallel character reversions and potentially also rampant gene flow with cultivated and/or naturally wild material. It hence poses great challenges for infraspecific classification, …

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Bioinformatics

Full text 2024

Complementing aculiferan mitogenomics: comparative characterization of mitochondrial genomes of Solenogastres (Mollusca, Aplacophora)

Bergmeier FS, Brachmann A, Kocot KM, et al.

<h4>Background</h4>With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class …

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Bioinformatics

Full text 2024

Charting the course for new discoveries in polyploid lineages

McKain M, Yang Y, Golicz A, et al.

No abstract available.

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Bioinformatics

Full text 2026

Genome analysis of Lactiplantibacillus plantarum and Levilactobacillus brevis isolated from traditionally fermented Ethiopian kocho and their probiotic properties

Mulaw G, Tesfay T, Sisay T, et al.

Probiotics are essential for promoting health, with lactic acid bacteria (LAB) from traditional fermented foods like Ethiopian kocho offering valuable benefits. The objective of this study was to systematically analyse the genomic characteristics, bacteriocin production, …

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Bioinformatics

Full text 2025

Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species

Wang TR, Ning X, Zheng SS, et al.

Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. <i>Quercus</i> is a keystone genus in Northern Hemisphere forests, and its wide …

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Bioinformatics Structural Variants Transcriptomics

Full text 2025

Evaluating the utility of deep genome skimming for phylogenomic analyses: A case study in the species-rich genus <i>Rhododendron</i>

Mo ZQ, Fu CN, Twyford AD, et al.

Deep genome skimming (DGS) has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses. However, its reliability with low DNA quality and quantity typical of archival specimens, such as herbarium …

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Bioinformatics

Full text 2025

Comparative genomics reveals details into the metabolism of peritrich ciliates (Ciliophora, Oligohymenophorea and Peritrichia)

de Souza PM, Cedrola F, Pedroso Dias RJ, et al.

The subclass Peritrichia encompasses over 1,000 species of ciliates, demonstrating both wide distribution and significant morphological diversity across aquatic environments. Despite their ecological significance and unique biological attributes, genomic information for peritrichs has remained sparse. …

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Bioinformatics

Full text 2025

Genomic and phenotypic insight into antimicrobial resistance of <i>Pseudomonas fluorescens</i> from King George Island, Antarctica

Silverio MP, Schultz J, Parise MTD, et al.

The genus <i>Pseudomonas</i> includes metabolically versatile microorganisms occupying diverse niches, from environmental habitats to plant pathogens, and has clinically significant strains. For this reason, <i>Pseudomonas</i> spp. might act as a reservoir of antimicrobial resistance genes, …

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Bioinformatics

Full text 2024

New mitochondrial genomes of three whip spider species from the Amazon (Arachnida, Amblypygi) with phylogenetic relationships and comparative analysis

Nogueira AF, Pires ES, Oliveira G, et al.

The complete mitochondrial genomes of the whip spiders Charinus carajas, C. ferreus, and Heterophrynus longicornis were sequenced, annotated, and compared with other mitogenomes of whip spiders and arachnids. The three new mitogenomes have the 37 …

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Bioinformatics

Full text 2024

A multi-million-year natural experiment: Comparative genomics on a massive scale and its implications for human health

Rivas-González I, Tung J.

Improving the diversity and quality of genome assemblies for non-human mammals has been a long-standing goal of comparative genomics. The last year saw substantial progress towards this goal, including the release of genome alignments for …

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Bioinformatics

Full text 2024

The Meaning and Measure of Concordance Factors in Phylogenomics

Lanfear R, Hahn MW.

As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci and therefore less sampling …

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Bioinformatics

Full text 2024

First Insight into the Whole Genome Sequencing Whole Variations in <i>Mycobacterium bovis</i> from Cattle in Morocco

Khoulane M, Fellahi S, Khayi S, et al.

Six cattle heads which tested positive against bovine tuberculosis (bTB) in Morocco were investigated to confirm the disease and to determine the source(s) of infection. Polymerase Chain Reaction (PCR) was directly performed on tissue samples …

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Bioinformatics

Full text 2024

Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

Thureborn O, Wikström N, Razafimandimbison SG, et al.

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a …

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Bioinformatics

Full text 2022

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data

Duchêne DA, Mather N, Van Der Wal C, et al.

The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic …

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Bioinformatics

Full text 2024

The genus Cortinarius should not (yet) be split

Gallone B, Kuyper TW, Nuytinck J.

The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius …

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Bioinformatics

Full text 2025

Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events

Romero Picazo D, Muccino F, Kwasigroch P, et al.

Plasmids are important drivers of evolutionary transformations and ecological adaptation in prokaryotes. Plasmids supplying the host with beneficial functions may become domesticated and gain a stable inheritance within the host lineage. Domesticated plasmids may comprise …

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Bioinformatics

Full text 2026

Phylogeography and population genetics of the white spotted eagle ray, Aetobatus laticeps Gill, 1865, in the Eastern Tropical Pacific

Vinueza Guarderas M, Torres ML, Pozo Andrade MJ, et al.

The Eastern Tropical Pacific (ETP) Spotted Eagle Ray, Aetobatus laticeps Gill, 1865, is an understudied species with limited information on its ecology and conservation status. Only in the last 10 years has this lineage been …

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Bioinformatics