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Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The …
Read PDFNon-tuberculous mycobacteria (NTM) represent an expanding group of environmental microorganisms with growing clinical significance, particularly among immunocompromised patients. In this study, we describe the isolation and comprehensive characterization of a novel Mycobacterium species, strain HUMS_1102779-3, …
Read PDFThis study reports the whole-genome sequence data and functional annotations of a novel <i>Stutzerimonas marianensis</i> strain LB-0542 isolated from the decomposing pelagic <i>Sargassum</i> biomass stranded on Long Beach, Barbados. The genomic DNA was sequenced with …
Read PDF<b>Background/Objectives</b>: <i>Bacteroides</i> species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical <i>Bacteroides</i> isolates from southern Thailand. <b>Methods</b>: Sixteen isolates were collected …
Read PDFThe advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree of life, yet achieving a complete species-level phylogeny remains a distant goal due to significant costs and computational demands. …
Read PDFWe present <i>Chlamydia trachomatis</i> Genome Assembly Pipeline (CtGAP) 2.0, an enhanced version of CtGAP, that provides a seamless installation process-eliminating the need for multiple standalone tools-and a streamlined command-line interface, introduces automatic assembly quality scoring …
Read PDFPhylogenomics pipelines are designed to reconstruct evolutionary relationships among groups of organisms. Existing pipelines are dependent upon reference gene sets for which target copies may be retrieved through read-mapping. This read-mapping approach is limited by …
Read PDFRoot-lesion nematodes (genus <i>Pratylenchus</i>) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to <i>Pratylenchus</i> genus …
Read PDFLong-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, …
Read PDF<i>Hibiscus syriacus</i>, a member of the tribe Hibisceae, is considered an important ornamental and medicinal plant in east Asian countries. Here, we sequenced and assembled the complete chloroplast genome of <i>H. syriacus</i> var. <i>Baekdansim</i> using …
Read PDFObtaining complete and accurate bacterial genomes is vital for studying the characteristics of uncultured bacteria. Single-cell genomics is a promising approach for the culture-independent recovery of bacterial genomes from individual cells. However, single-amplified genomes (SAGs) …
Read PDFLong-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational …
Read PDF<i>Borrelia miyamotoi</i> is an emerging <i>Ixodes</i> tick-borne human pathogen in the Northern hemisphere. The aim of the current study was to compare whole genome sequences of <i>B. miyamotoi</i> isolates from different continents. Using a combination …
Read PDFThe large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable …
Read PDF<b>Background:</b> Population-specific reference genomes are essential for improving the accuracy and reliability of genomic analyses across diverse human populations. Although Vietnam ranks as the 16th most populous country in the world, with more than 86% …
Read PDFCryptosporidium parvum is a zoonotic parasite of the intestine and poses a threat to human and animal health. However, it is difficult to obtain a large number of oocysts for genome sequencing using in vitro …
Read PDFLong-read sequencing is a valuable technique for high-precision genome analysis. Despite the widespread use of the <i>Mycobacterium tuberculosis</i> H37Rv genome sequence as a reference for genetic variation analysis, its suitability for comparing clinical strains is …
Read PDFMuseum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, …
Read PDFStructural variants (SVs) play a critical role in shaping the diversity of the human genome, and their detection holds significant potential for advancing precision medicine. Despite notable progress in single-molecule long-read sequencing technologies, accurately identifying …
Read PDF<h4>Abstract</h4>Hemophilia is an X-linked bleeding disorder caused by defects in the F8 or F9 genes. Given the wide variety of F8 variants, conventional genetic testing typically requires a combination of multiple methods, and detecting rearrangements …
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