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Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs
In recent years, the increase in genome sequencing across diverse plant species has provided a significant advantage for phylogenomics studies, allowing the analysis of one of the most diverse gene families in plants: nucleotide-binding leucine-rich …
Read PDFExploring the Potential and Evaluating Hydrocarbon Degradation by Novel Antarctic Dietzia and Pusillimonas Isolates From a Pristine Environment
This study evaluated the bioremediation potential of two psychrotolerant strains, Pusillimonas sp. ANT_WB101 and Dietzia sp. ANT_WB102, isolated from an uncontaminated water pond. Comparative analysis indicated affinities with P. gingsengisoli/soli and D. kunjamensis/maris. Both strains …
Read PDFThe complete mitochondrial genome of the pulmonate snail <i>Melampus sincaporensis</i> (Gastropoda: ellobiidae) from South Korea
The pulmonate snail <i>Melampus sincaporensis</i> L. Pfeiffer, 1855 (Gastropoda: Ellobiidae) lives in extreme environments such as salt marshes with limited oxygen. Here, we characterized the complete mitochondrial genome of <i>M. sincaporensis</i> from South Korea. It …
Read PDFHigh-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom <i>Stropharia rugosoannulata</i>
<i>Stropharia rugosoannulata</i>, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality …
Read PDFPhylogenomics redefines the evolutionary history of mosquitoes
Mosquitoes have a substantial impact on human and animal health, but their deeper evolutionary relationships have been difficult to resolve. We inferred a time-calibrated phylogenetic history of mosquitoes using conserved genome-wide markers from representatives of …
Read PDFPhylogenetic and Divergence Time Estimation of Muscomorpha with Low-Coverage Whole-Genome Sequencing of Syrphidae (Diptera: Brachycera)
Muscomorpha is one of the most diverse groups in Brachycera, yet its higher-level phylogenetic relationships remain controversial, primarily concerning the monophyly and placement of Syrphoidea, the position of Platypezoidea, internal relationships in Calyptratae and Acalyptratae, …
Read PDFThe Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes
Understanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the genus Gouania provide an excellent system to study …
Read PDFUltraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non-Model Nematodes
Nematodes are among the most diverse animals, yet only around 28,000 of an estimated one million species have been morphologically described. Their small size, morphological simplicity, and cryptic diversity complicate phylogenetic analyses. Traditional morphological and …
Read PDFThe Explosive Radiation of the Neotropical Tillandsia Subgenus Tillandsia (Bromeliaceae) Has Been Accompanied by Pervasive Hybridization
The recent rapid radiation of Tillandsia subgenus Tillandsia (Bromeliaceae) provides an attractive system to study the drivers and constraints of species diversification. This species-rich Neotropical monocot clade includes predominantly epiphytic species displaying vast phenotypic diversity. …
Read PDFPhylogenomics reveals the evolution of floral traits associated with pollinators and pollinator-prey conflict within the carnivorous Pinguicula subgenus Temnoceras
<h4>Premise</h4>The carnivorous plant genus Pinguicula (Lentibulariaceae) exhibits remarkable floral diversity associated with pollination, particularly in the largest subgenus Temnoceras, which spans Mexico and Central America. Despite this diversity, the relationships between species and the evolution …
Read PDFComparative Genomics and Phylogenomics of Novel Radiation-Resistant Bacterium <i>Paracoccus qomolangmaensis</i> sp. nov. S3-43<sup>T</sup>, Showing Pyrethroid Degradation
This study focused on the multifunctional characteristics and bioremediation potential of <i>Paracoccus</i> spp. A novel Gram-stain-negative, aerobic, non-motile, ellipsoidal bacterium, named <i>Paracoccus qomolangmaensis</i> S3-43<sup>T</sup>, was isolated from moraine samples collected from the north slope of …
Read PDFSpecies-Discriminating Diagnostic PCR, Ribosomal Intergenic Spacer-Based Single-Marker Taxonomy and Cryptic Descriptions of the Fungal Entomopathogens <i>Metarhizium hybridum</i> and <i>Metarhizium parapingshaense</i>
(1) Background: Potentially arthropod-pathogenic and plant-associated <i>Metarhizium</i> fungi are of high interest for basic research, biological pest control and plant growth promotion. Unambiguous species delineation enabling the taxonomic assignment of new isolates and the identification …
Read PDFPhylogenomics unravels the early divergence and diversification in Bignoniaceae
Bignoniaceae, a pantropical family comprising 79 genera and 901 species, exhibits remarkable morphological and ecological diversity, including lianas, shrubs, trees, and high-elevation herbs. Reconstructing the early evolutionary history of Bignoniaceae has been particularly challenging due …
Read PDFRelative performance of three phylogenetic methods based on complete mitochondrial genomes of barnacle
Mitochondrial Genome analysis is essential for understanding phylogenetic relationships. However, few studies have compared the performance of phylogenetic approaches for marine invertebrates, which have a complex evolutionary history. This study compared three phylogenetic trees based …
Read PDFGenomic Insights into a New Burkholderia cenocepacia Sequence Type Linked to Cepacia Syndrome in Cystic Fibrosis
Burkholderia cenocepacia is an important pathogen in cystic fibrosis (CF) patients, responsible for chronic lung infections and, in severe cases, cepacia syndrome (CS), characterized by necrotizing pneumonia, bacteremia, and high mortality. Epidemic lineages, such as …
Read PDFPlastid and nuclear phylogenomics of Cyphostemma (Vitaceae) provide new insights into genome size evolution across sub-Saharan Africa
Genome size, the total amount of DNA content in the cell nucleus, varies greatly among flowering plants. One factor underlying this variation is the environment under which plants evolve. Given this premise, harsh environmental conditions …
Read PDFGenomic profiling of ESBL/AmpC-producing <i>Escherichia coli</i> from backyard poultry: resistome, virulome, plasmidome, and CRISPR-Cas insights
<h4>Introduction</h4>Antimicrobial resistance (AMR) is a major One Health concern driven by many factors including unregulated animal farming. This study aimed to perform a comprehensive phenotypic and genotypic characterization of <i>Escherichia coli</i> isolated from backyard poultry …
Read PDFPlastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence
<h4>Background</h4>Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, and medicinal components, there has been limited research …
Read PDFHigh Prevalence of Ceftriaxone-Resistant Neisseria gonorrhoeae in Hanoi, Vietnam, 2023-2024
Ceftriaxone resistance in Neisseria gonorrhoeae is an escalating global health concern, threatening the efficacy of empiric treatment. In the Asia-Pacific region, a rapid surge in ceftriaxone resistance has been observed, primarily associated with the penA-60.001 …
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