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We report the antimicrobial susceptibility profile and genomic features of the <i>Salmonella enterica</i> serovar Rissen strain FARPER-637 isolated from Peruvian swine in 2025. Nanopore sequencing revealed blaTEM-1B, tet(A), and qnrB19. Phenotype-genotype concordance was observed except …
Read PDFThis study reports an optimized in-house 2-step PCR-SSP assay for rapid, cost-effective detection of <i>HLA-B*57:01</i> and <i>HLA-B*58:01</i> in routine pharmacogenomics laboratory. This assay employs allele-specific primers positioned within exon 2-3 boundaries, validated <i>in silico</i> against …
Read PDFThe first haplotype-resolved chromosome-scale genome assembly for the bighead catfish (Clarias macrocephalus), a freshwater species native to Thailand and Vietnam, which has importance in aquaculture and conservation, is presented here. The 880 Mb genome was …
Read PDFFolsomia candida (Collembola: Isotomidae) is one of the most important indicator species for soil animal studies and is widely distributed worldwide. Here, we utilized PacBio HiFi long reads, Oxford Nanopore Technologies (ONT) ultralong reads, Hi-C, …
Read PDFDNA methylation is crucial for genome regulation and provides key insights into the interaction between genetics and environmental factors, offering valuable perspectives for ecological research. However, knowledge of DNA methylation patterns in nonmodel invertebrates remains …
Read PDFIn recent years, the quality of genome assemblies has notably improved, primarily due to advances in third-generation sequencing technologies and bioinformatics tools. In the present study, we obtained genome assemblies for two flax (<i>Linum usitatissimum</i> …
Read PDF<h4>Background</h4>Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are …
Read PDFOxford Nanopore direct-RNA sequencing, a third-generation sequencing technology, allows for the analysis of native RNA molecules in their natural cellular state. However, cellular RNA is predominantly composed of ribosomal RNA and transcripts from ubiquitously expressed …
Read PDFAs a First-Class Protected species in China, the Tibetan wild ass (Equus kiang) is endemic to the Qinghai-Tibet Plateau and exhibits remarkable adaptation to extreme high-altitude environments characterized by low oxygen, cold temperatures, and high …
Read PDFHere, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: (i) Improved variant discovery and genotyping through partial order multiple …
Read PDF<h4>Background</h4>Clonotyping of immunoglobulin heavy chain (IGH) gene rearrangements is critical for diagnosis, prognostication, and measurable residual disease monitoring in chronic lymphocytic leukemia (CLL). Although short-read next-generation sequencing (NGS) platforms, such as Illumina MiSeq, are widely …
Read PDFThe complexity of potato genetics, characterised by tetrasomic inheritance, has contributed to slower genetic gain in potato compared to other major crops. Disease resistance genes, often found in large clusters of highly similar paralogs and …
Read PDFExtrachromosomal circular DNA (eccDNA) is a type of circular DNA that exists independently of chromosomes and has garnered significant attention in various fields, particularly in the context of smaller eccDNAs, which have considerable roles in …
Read PDFHigh-throughput sequencing datasets frequently exhibit extreme read depth variation, biasing downstream analysis. Normalising coverage to a specific depth cap is important, yet existing tools rely on computationally expensive fetch-based or non-deterministic greedy algorithms. Here, we …
Read PDFThe order Siluriformes, a hyperdiverse teleost clade with over 3,000 species, exemplifies adaptive radiation through significant phenotypic innovations such as aerial respiration. However, the limited availability of high-quality genomes, particularly in underrepresented families such as …
Read PDF<h4>Motivation</h4>In prokaryotic genomes, methylation is an important epigenetic modification that regulates the uptake of foreign DNA; it can also contribute to replication or virulence. We present MPore, a novel method for the database-driven detection of …
Read PDFRare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, …
Read PDFHere, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a combination of Oxford Nanopore long-read and Illumina short-read sequencing. Yarrowia lipolytica is an industrially …
Read PDFThe fourfinger threadfin (Eleutheronema tetradactylum) is a euryhaline fish distributed across the Indo-West Pacific, from the Persian Gulf to Australia. However, the lack of high-quality genomic resources has limited genomic-level studies of its evolution, conservation, …
Read PDFThe Steppe Eagle, <i>Aquila nipalensis</i> Hodgson, 1833, is a migratory, endangered raptor experiencing population declines due to habitat loss and human persecution. This study aims to construct a high-quality <i>de novo</i> nuclear genome and complete …
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