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We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci-such as genes, proteins, genomic segments, and positions-as parameters. Using the …
Read PDFWe present a genome assembly from an individual of <i>Inga leiocalycina</i> (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 948.00 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. …
Read PDFThe Latin American Coalition for Escherichia coli Research (LACER) was created as a network of investigators using One Health approaches trying to understand infections caused by regional E. coli isolates and to sound the alarm …
Read PDF<b>Background/Objectives:</b><i>Acinetobacter baumannii</i> is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant <i>A. baumannii</i> (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk …
Read PDFThe subtribe Leptoboeinae (Gesneriaceae: Trichosporeae) comprises seven genera-<i>Rhynchotechum</i> Blume, <i>Boeica</i> C.B.Clarke, <i>Beccarinda</i> Kuntze, <i>Leptoboea</i> Benth., <i>Platystemma</i> Wall., <i>Crassicaulis</i> Lei Cai & Mich.Moller, and <i>Championia</i> Gardner. It is highly valuable in horticulture and medicine. However, long-standing …
Read PDF<i>Xanthoparmelia</i> (Vain.) Hale is one of the two hyperdiverse genera in the family Parmeliaceae, with over 500 species and a wide distribution. In this study, we sequenced, assembled, and annotated the complete mitochondrial genomes of …
Read PDF<h4>Background</h4>In 2018, the island of Mayotte located in the western Indian ocean, has experienced a seismo-volcanic crisis linked to the birth of an impressive intraplate submarine volcano at the east of the island. This volcano, …
Read PDFSome species of the Leucosphyrus Group of Anopheles mosquitoes in Southeast Asia are highly anthropophilic and efficient vectors of human malaria parasites, while others primarily feed on non-human primates (NHP) and transmit NHP malaria parasites. …
Read PDFThe genus Erythronium L. (Liliaceae) comprises approximately 30 species of spring-flowering perennial herbs that are widely distributed in temperate areas across the Northern Hemisphere. Although species within the genus exhibit considerable morphological similarity, their phylogenetic …
Read PDFPhylogenetic tip-dating has been and still is revolutionizing evolutionary biology in several ways. Fossil tip-dating, where fossils are placed into a phylogeny as tips based on morphological and/or molecular character information, provides a more principled …
Read PDFCrabgrasses (Digitaria spp.) rank among the most invasive upland weeds globally, exhibiting remarkable ecological plasticity. To uncover the genomic basis underlying their weediness and environmental adaptability, we generate a telomere-to-telomere (T2T) reference genome of Digitaria …
Read PDFThe emergence of multidrug-resistant <i>Staphylococcus aureus</i> (MDR-<i>S. aureus</i>) demands innovative strategies to identify robust microbial producers of potent antibiotics. This study characterizes <i>Streptomyces virginiae</i> THA-960, a soil-derived actinomycete, as a producer of the known anti-MDR-<i>S. …
Read PDFRelating billions of proteins across the tree of life remains a challenging task for comparative biosphere genomics and artificial intelligence-driven structure prediction. Here we present DIAMOND DeepClust, a cascaded, ultra-fast clustering method enabling planetary-scale organization …
Read PDFBACKGROUND: Escherichia coli (E. coli) is a leading cause of bloodstream infections (BSIs) globally, with multidrug-resistant (MDR) strains complicating treatment outcomes. In South Africa, genomic data on such isolates remain scarce. To elucidate the genomic …
Read PDFWhile mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, …
Read PDFThe genus <i>Tuber</i> (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive …
Read PDFA novel moderately halophilic and alkaliphilic Gram-stain-negative, strictly aerobic, bacterial strain (N2<sup>T</sup>) was isolated from an inland saltern in central Portugal. The taxonomic position of this isolate was determined based on polyphasic taxonomic and phylogenomic …
Read PDF<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) …
Read PDF<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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