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The assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these …
Read PDFThe incidence of infections caused by multidrug-resistant <i>E. coli</i> strains has risen in the past years. Antibiotic resistance in <i>E. coli</i> is often mediated by acquisition and maintenance of plasmids. The study of <i>E. coli</i> …
Read PDFBacteriophage receptor-binding proteins are often attached to the tail via a conserved N-terminal adapter/anchor domain, presumed to function independently from the distal receptor-binding/catalytic domain. Using synthetic phage technology, we demonstrated that the N-terminal domain in …
Read PDFBy limiting the efficacy of selection, random drift is expected to play a major role in genome evolution. Formalizing this idea, the nearly-neutral theory predicts that the ratio of non-synonymous over synonymous polymorphism (πN/πS) within …
Read PDFIn the context of public health, asymptomatic carriers of respiratory infectious diseases are considered a hidden yet critical factor in the transmission of infection and represent a key target for efforts to mitigate disease spread. …
Read PDF<h4>Purpose</h4>This study aims to investigate the antibiotic resistance and virulence factors of <i>Paenibacillus campinasensis</i>, an understudied opportunistic pathogen, through whole-genome sequencing and resistance genes. The findings will contribute to the development of effective clinical strategies …
Read PDF<i>Limosilactobacillus reuteri</i> is a lactic acid bacterium with several probiotic properties. Here, we present the draft genome sequence of <i>L. reuteri</i> isolated from the porcine ileum with a genome size of 2.1 Mb. The average …
Read PDF<i>Klebsiella variicola</i> strain YSP4_INTEC was isolated from a Dominican Republic River and had its genome sequenced (size: 5,611,899 bp and GC content: 57.19%). The genomic analysis identified various genes involved in plant colonization mechanisms, plus …
Read PDF<h4>Summary</h4>Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, …
Read PDFHere, we present whole genome sequencing (WGS) data of clinical <i>Klebsiella pneumoniae</i> and <i>K. quasipneumoniae</i> isolates obtained from urine samples collected between October 2024 and January 2025 from patients in hospitals in Baghdad, Iraq. A …
Read PDFBACKGROUND: Marine-derived fungi are prolific producers of structurally diverse secondary metabolites with significant pharmaceutical potential. The discovery of natural products has been unprecedentedly accelerated by the prediction of biosynthetic gene clusters (BGCs) within the whole-genome …
Read PDFThe Y chromosome evolves rapidly, often differing dramatically even between closely related species. While such divergence has long been suspected to contribute to hybrid male sterility, leading to reproductive isolation and thus speciation, the underlying …
Read PDFThe genus Skeletonema stands out as one of the most prevalent and globally distributed diatoms within coastal marine ecosystems. Additionally, it holds significance as a pivotal organism across diverse research domains, encompassing biochemistry, ecophysiology, molecular …
Read PDF<i>Candida parapsilosis</i> is a major pathogen causing central venous catheter-associated bloodstream infections with biofilm formation as virulence factor. We sequenced the genomes of six <i>C. parapsilosis</i> isolates from bloodstream infections displaying no, low, and high …
Read PDFWe report draft genome sequences of 12 <i>Agrobacterium</i> strains isolated from coastal plants in Taiwan. Assemblies range from 4.95 to 5.42 Mb with >97.5% completeness. Genomic analyses reveal species identities and secretion system genes, providing …
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Read PDF<h4>Summary</h4>Bioinformatics is a rapidly evolving field with numerous specialized tools developed for essential genomic analysis tasks, such as read simulation, mapping, and variant calling. However, managing these tools presents significant challenges due to varied dependencies, …
Read PDFThis study reports the draft genome sequence of <i>Pseudomonas</i> sp. MAHUQ-62, a bacterial strain isolated from the soil sample of a pumpkin garden located in Anseong, South Korea, in 2020. The genome consists of 6,038,011 …
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