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Whole-genome studies in cattle play a key role in exploring both individual and population-level genetic variability. Recently, low-coverage whole-genome sequencing (0.5-2×) has been considered as an alternative to traditional approaches. Low-coverage whole-genome sequencing (lcWGS), which …
Read PDF<h4>Motivation</h4>Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in …
Read PDFWild carnivores can harbor pathogens affecting wildlife conservation and domestic animal health. This study surveyed major viral pathogens in free-ranging wolves, red foxes, stone martens, and Eurasian badgers in Northwestern Italy. Duodenal samples from 140 …
Read PDFOff-white or yellowish shoots are common in tea plants (<i>Camellia sinensis</i> L.), and such albino variations are often accompanied by metabolic reprogramming, including increased contents of amino acids and lower levels of polyphenols. Nonetheless, the …
Read PDF<i>Rhodotorula pacifica</i> INDKK, an oleaginous red yeast isolated from mangrove forest soil, efficiently metabolizes biomass hydrolysates and accumulates lipids of more than 60% of its dry weight. Hybrid <i>de novo</i> genome assembly (Illumina and Oxford …
Read PDFLong-read amplicon profiling through read classification limits phylogenetic analysis of amplicons while community analysis of multicopy genes, relying on unique molecular identifier (UMI) corrections, often demands deep sequencing. To address this, we present a long …
Read PDFBiodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches …
Read PDFDuring the COVID-19 pandemic, stringent public health measures led to historically low influenza activity in Hong Kong. However, after these interventions were relaxed in 2023, Influenza A viruses (IAV), including A(H1N1)pdm09 and A(H3N2), rapidly resurfaced. …
Read PDFThird-generation sequencing technologies have revolutionized the study of epigenetic characteristics in human diseases, with Oxford Nanopore Technologies (ONT) at the forefront of long-read sequencing. ONT has made rapid improvements in flow cell designs, which greatly …
Read PDFThe endangered mountain gorilla, Gorilla beringei beringei, faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for …
Read PDF<h4>Objective</h4>This study presents the whole genome sequence of Staphylococcus aureus strain 37M isolated from cows with subclinical mastitis in Kiruhura district, Uganda. The objective was to characterize the genome to understand the isolate's resistance and …
Read PDFInfluenza A virus (IAV) remains a major health concern in both humans and animals, with pigs serving as key reservoirs for generating novel reassortant viruses with pandemic potential. Respiratory microbiome alterations during infection may facilitate …
Read PDF<b>Background/Objectives</b>: Rapid and accurate pathogen identification and antimicrobial susceptibility testing (AST) are critical for the proper management of patients with bloodstream infection (BSI). Real-time whole-genome sequencing (WGS) represents an attractive opportunity for exhaustive pathogen identification …
Read PDFThe selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes …
Read PDFSomatic cell nuclear transfer (SCNT) holds promise for animal cloning but remains limited by low efficiency and phenotypic abnormalities, often attributed to incomplete nuclear reprogramming. This study presents an integrative genomic and epigenomic analysis of …
Read PDFSevere acute respiratory infection (SARI) remains one of the leading causes of morbidity and mortality worldwide. Multiple viruses can cause this infection. Sequencing technologies hold great promise for detecting viral pathogens. This proof-of-concept study aimed …
Read PDFAntimicrobial-resistant (AMR) <i>Klebsiella</i> spp., the common agents of nosocomial infections, are on the rise and becoming increasingly dangerous, with tigecycline-resistant strains posing a serious clinical threat. This study aimed to characterize isolated tigecycline-resistant strains from …
Read PDFThe isolation of locally adapted rhizobial strains with high symbiotic activity represents an effective strategy for increasing soybean yield under extreme environmental conditions. In this study, seven novel strains were isolated from nodules of soybeans …
Read PDF<h4>Background</h4>Whole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use …
Read PDFNorwegian Red (NR) cattle are the main dairy breed in Norway, bred according to a broad breeding goal including health and fertility since the 1970s. Genomic studies on NR cattle have relied on the public …
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