Editorial: Soilborne pathogenic fungi: systematics, pathogenesis and disease control
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Genomic and proteomic analyses of Nus-dependent non-lambdoid phages reveal a novel coliphage group prevalent in gut: mEp<sub>immI</sub>
<h4>Introduction</h4>Nus-dependent Mexican <i>Escherichia coli</i> phages (mEp) were previously isolated from clinical samples of human feces. Approximately 50% corresponded to non-lambdoid temperate phages integrating a single immunity group, namely immunity I (mEp<sub>immI</sub>), and these were as …
Read PDFBetaAlign: a deep learning approach for multiple sequence alignment
<h4>Motivation</h4>Multiple sequence alignments (MSAs) are extensively used in biology, from phylogenetic reconstruction to structure and function prediction. Here, we suggest an out-of-the-box approach for the inference of MSAs, which relies on algorithms developed for processing …
Read PDFMulti-locus phylogenetic network analysis of Ampelomyces mycoparasites isolated from diverse powdery mildews in Australia and the generation of two de novo genome assemblies
The interactions between powdery mildews (Ascomycota, Erysiphaceae), obligate biotrophic pathogens of many plants, and pycnidial fungi belonging to the genus Ampelomyces, are classic examples of specific mycoparasitic relationships. These interactions are common and finely tuned …
Read PDFPlastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales
<h4>Background</h4>The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. …
Read PDFGenomic perspectives on the global dissemination of Elizabethkingia anophelis: unveiling inherent multidrug resistance and virulence determinants
BACKGROUND: Elizabethkingia anophelis has emerged as a formidable pathogen responsible for severe, life-threatening infections in immunocompromised populations. However, the genetic underpinnings of its virulence and antimicrobial resistance remain poorly characterized. Leveraging our previously assembled collection …
Read PDFA chromosomal-level genome assembly of Thanatophilus sinuatus Fabricius (Coleoptera: Staphylinidae)
Thanatophilus sinuatus (Coleoptera: Staphylinidae), a widespread necrophagous beetle frequently recovered from remains, is critical for post-mortem interval estimation. The absence of a reference genome has limited molecular studies of its forensic traits. Here, we report …
Read PDF<i>Berberisjiuzhaigouensis</i> (Berberidaceae), a new riparian shrub from northern Sichuan, China
<i>Berberisjiuzhaigouensis</i> is herein described as a new deciduous species endemic to riparian habitats in Jiuzhaigou, northern Sichuan, China. Phylogenetic analyses based on complete plastome sequences and 322 nuclear loci consistently recover <i>B.jiuzhaigouensis</i> as a distinct …
Read PDFComplete Chloroplast Genome of <i>Enkianthus</i> Lour. (Ericaceae): Comparative Analysis, Phylogenetic Relationships, Divergence History, and Adaptive Evolution
<i>Enkianthus</i> (Ericaceae) is a small genus of great ornamental and ecological importance, preferring the specialized habitats in montane elfin forests of east Asia. Here, we for the first time sequenced, assembled, and annotated the complete …
Read PDFPhylogenomics of the gray-breasted sabrewing (Campylopterus largipennis) species complex in the Amazonia and Cerrado biomes
The Neotropics are one of the most biodiverse regions of the world, where environmental dynamics, climate and geology resulted in a complex diversity of fauna and flora. In such complex and heterogeneous environments, widely distributed …
Read PDFThe genome sequence of the common water plantain, <i>Alisma plantago-aquatica</i> L. (Alismataceae)
We present a genome assembly from a specimen of <i>Alisma plantago-aquatica</i> (common water plantain; Streptophyta; Magnoliopsida; Alismatales; Alismataceae). The genome sequence has a total length of 9,377.97 megabases. Most of the assembly (99.53%) is scaffolded …
Read PDFMultidimensional Gene Space as an Approach for Analyzing the Organization of Genomes
Genomic organization and its comparative analysis throughout all major kingdoms of life are extensively studied across multiple scales, ranging from individual gene-level analyses to system-wide investigations. This work introduces a novel framework for characterizing genetic …
Read PDFAn integrative view on the systematic position of the cupressophyte <i>Cephalotaxus</i>
We made an in-depth review of historical studies of the cupressophyte conifer genus <i>Cephalotaxus</i> Siebold & Zucc. with an emphasis on its systematic position. We suggest that the systematic position of the genus is better …
Read PDFThe genome sequence of a beetle, <i>Brachypterus glaber</i> (Newman, 1834)
We present a genome assembly from an individual female specimen of <i>Brachypterus glaber</i> (beetle; Arthropoda; Insecta; Coleoptera; Kateretidae). The genome sequence has a total length of 648.30 megabases. Most of the assembly (95.55%) is scaffolded …
Read PDFDistribution and evolutionary significance of the DnaK-DnaJ-GrpE (KJE) chaperone system in archaea
A prevailing hypothesis for the emergence of life on Earth holds that it might have originated in hydrothermal vents, where the environmental conditions, although physically and chemically extreme (acidity, lack of oxygen, high pressure, very …
Read PDFDraft genome sequences for ten strains of <i>Xanthomonas</i> species that have phylogenomic importance
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: <i>Xanthomonas campestris</i> pv. <i>asclepiadis</i>, <i>X. campestris</i> pv. <i>cannae</i>, <i>X. campestris</i> pv. <i>esculenti</i>, <i>X. campestris</i> pv. <i>nigromaculans</i>, <i>X. campestris</i> pv. <i>parthenii</i>, <i>X. …
Read PDFFunctional and genomic characterization of polyethylene degrading yeast Meyerozyma carpophila M6.0.2 isolated from marine plastic debris in East Java Indonesia
Polyethylene (PE) is a primary contributor to environmental plastic pollution, posing a critical risk to ecosystems and living organisms. This study screened six yeast strains (BI.4.1.1, K3.1.2, M.5.0.1, M.5.0.3, M.6.0.1, and M.6.0.2) isolated from marine …
Read PDFGenomics of Irish swine-derived <i>Streptococcus suis</i>: population structure, prophages and anti-viral defence mechanisms
<i>Streptococcus suis</i> is a major pig pathogen with zoonotic potential, posing an occupational risk to farmers and meat handlers. We characterized 110 <i>S</i>. <i>suis</i> strains from diseased pigs in Ireland (2005-2022) using whole-genome sequencing to …
Read PDF<i>Phaeodactylum tricornutum</i> as a Chassis: Insights into Its Potential, Challenges, and Perspectives
<i>Phaeodactylum tricornutum</i> is one of the most well-characterized microalgae and serves as a pivotal model diatom in global carbon fixation and the mediation of biogeochemical cycling of essential nutrients. Over the past few decades, the …
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