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Full text 2024

Unraveling the Complete Mitochondrial Genome of <i>Potamalpheops Sp.</i> (Purple Zebra Shrimp) (Crustacea: Decapoda) Provides Insights Into Its Phylogenetic Relationships and Gene Order Rearrangements

Das SP, Kao YK, Nguyen HT, et al.

Understanding the functions of mitochondrial genomes is crucial for studies related to the evolution of genomes, phylogenomics, and species identification. For the first time, complete mitogenome of <i>Potamalpheops sp.</i> a non-snapping shrimp has been successfully …

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Bioinformatics
Full text 2025

Genomic characterization of multidrug-resistant &lt;i&gt;Escherichia albertii&lt;/i&gt; of fish origin-first isolation and insights into a potential food safety threat

Srinivas K, Ghatak S, Milton AAP, et al.

<h4>Introduction</h4><i>Escherichia albertii</i> is an emerging food-borne pathogen with zoonotic potential which is often under-reported due to misidentifications.<h4>Materials and methods</h4>The current study identified <i>E. albertii</i> from retail fish sold in market which was confirmed by phenotypic …

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Bioinformatics
Full text 2026

Evolutionary and Mobile Genetic Element Analysis of a Multidrug-Resistant ST398-MRSA-Vc Isolate from Ready-to-Eat Pork Products

Wan J, Wang X, Wang K, et al.

<b>Background:</b> Livestock-associated methicillin-resistant <i>Staphylococcus aureus</i> (LA-MRSA) ST398 poses a significant zoonotic threat, largely due to its capacity to acquire and disseminate antimicrobial resistance through mobile genetic elements (MGEs). Ready-to-eat (RTE) foods may serve as critical …

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Bioinformatics
Full text 2025

Integrated Genetic Characterization and Quantitative Risk Assessment of Cephalosporin- and Ciprofloxacin-Resistant &lt;i&gt;Salmonella&lt;/i&gt; in Pork from Thailand

Kiatyingangsulee T, Hein ST, Prathan R, et al.

<b>Background/Objectives</b>: This study assessed the risk associated with third-generation cephalosporin- and fluoroquinolone-resistant <i>Salmonella</i> from pork consumption by integrating phenotypic resistance profiles with genetic data to characterize the risks and transmission pathways. <b>Methods</b>: <i>Salmonella</i> were isolated …

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Bioinformatics
Full text 2024

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data

Duchêne DA, Duchêne S, Stiller J, et al.

Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals …

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Bioinformatics
Full text 2023

Phylogenomics and phylogeography of <i>Menispermum</i> (Menispermaceae)

Song S, Cameron KM, Wang Y, et al.

<h4>Introduction</h4>Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant …

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Structural Variants
Full text 2025

Ecological speciation with gene flow followed initial large-scale geographic speciation in the enigmatic afroalpine giant senecios (Dendrosenecio)

Gorospe JM, Záveská E, Chala D, et al.

Mountains have highly heterogeneous environments that generate ample opportunities for lineage differentiation through ecological adaptation, geographic isolation and secondary contact. The geographic and ecological isolation of the afroalpine vegetation fragments on the East African mountain …

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Bioinformatics
Full text 2026

Resolving taxonomic uncertainties in the genus &lt;i&gt;Haemophilus&lt;/i&gt;: a genomics-based approach for the reclassification of species within genera of the family &lt;i&gt;Pasteurellaceae&lt;/i&gt; and proposal of four novel genera and one novel species

Seguí G, Piñeiro-Iglesias B, Salvà-Serra F, et al.

<h4>Introduction</h4>The taxonomy of species within the genus <i>Haemophilus</i>, within the family <i>Pasteurellaceae</i>, shows extensive polyphyly, causing long-standing taxonomic ambiguities that complicate clinical, epidemiological and evolutionary research. Traditional classifications based on phenotypes and comparative 16S rRNA …

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Bioinformatics Metagenomics
Full text 2025

Hepatincolaceae (Alphaproteobacteria) are Distinct From Holosporales and Independently Evolved to Associate With Ecdysozoa

Castelli M, Gammuto L, Podushkina D, et al.

The Hepatincolaceae (Alphaproteobacteria) are a group of bacteria that inhabit the gut of arthropods and other ecdysozoans, associating extracellularly with microvilli. Previous phylogenetic studies, primarily single-gene analyses, suggested their relationship to the Holosporales, which includes …

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Bioinformatics