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Highly pathogenic avian influenza (HPAI) poses a major threat to the world economy and human health; hence, rapid and accurate identification of avian influenza virus (AIV) subtypes is required for effective surveillance and outbreak prevention, …
Read PDFWe present the complete genome sequence of Sphingomonas sp. gentR, a strain exhibiting high-level resistance to gentamicin (MIC = 40 mg/mL). The genome was assembled from hybrid Illumina and Nanopore sequencing data into a gap-free …
Read PDFReal-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source …
Read PDFTicks pose substantial threats to public health. Blacklegged ticks (Ixodes scapularis) are responsible for most tick-borne diseases in the US, transmitting seven human pathogens, including the etiological agent of Lyme disease, Borrelia burgdorferi. Molecular surveillance …
Read PDF<h4>Motivation</h4>Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics due to its capacity to generate complete genome information. However, there is a lack of robust and easy-to-use pipelines for comprehensive LRS …
Read PDFThe bumble bee wax moth, Aphomia sociella, is an important lepidopteran pest impacting bee colonies essential for pollination and apiculture. Like other moths, this species has been reported to ingest plastics. Although specific enzymes have …
Read PDFRapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi<sup>®</sup>) software for detection of nine RNA …
Read PDFModern genetics increasingly relies on genomic data sets to address medical, ecological, and evolutionary questions. Investigating these questions requires a diverse set of core competencies in wet-lab techniques, data analysis, and bioinformatics. We describe the …
Read PDFHalisarca dujardinii is a marine sponge known for its ability to completely regenerate via cell reaggregation. Here we present the first chromosome-level genome assembly of H. dujardinii, generated using Oxford Nanopore long reads, Illumina short …
Read PDFDiagnostic testing of foot-and-mouth disease virus (FMDV) currently utilizes reverse transcription quantitative PCR (RT-qPCR) to detect the presence of viral RNA and double antibody sandwich ELISAs (DAS-ELISAs) to determine viral serotype. Serotype identification is critical …
Read PDF<i>Lysobacter antibioticus</i> Hz25 is a novel strain that was isolated from the rhizosphere of the relict endemic plant <i>Hedysarum zundukii</i> Peschkova (Fabaceae), which grows on carbonate soils in the Baikal region of Russia. This work …
Read PDFThe mandarin fish (Siniperca scherzeri), renowned as the "freshwater grouper", has emerged as a commercially significant aquaculture species in China due to its superior flesh quality, disease resistance, and domestication adaptability. With the rapid development …
Read PDFRecent advancements in sequencing technologies have transformed the characterization of genomic and transcriptomic complexity. In this review, we present a comprehensive overview of Oxford Nanopore Technologies (ONT), emphasizing its unique capability for real-time, long-read, and …
Read PDF<h4>Purpose</h4>Drug-resistant tuberculosis (DR-TB) complicates treatment and requires diagnostic approaches capable of comprehensive resistance profiling of <i>Mycobacterium tuberculosis</i> (MTB). This study evaluated the diagnostic performance of the Oxford Nanopore Technologies (ONT) custom TB-DR sequencing assay, a …
Read PDFNanopore sequencing provides long and ultra-long reads that are valuable for structural variation (SV) detection and genome assembly. However, false-positive chimeric reads can arise and interfere with somatic SV calling. Here, we show that ligation-based …
Read PDF<h4>Motivation</h4>High-quality genome annotations are essential for transcriptomic analyses investigating plant responses to environmental stress. While nanopore long-read direct RNA sequencing offers a powerful approach for improving genome annotations, studies benchmarking optimal tools for this process …
Read PDFCassava mosaic disease (CMD), caused by begomoviruses such as African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), poses a threat to food security in sub-Saharan Africa. Conventional PCR assays often fail …
Read PDF<h4>Background</h4>The ribosomal DNA (rDNA) of the myxomycete Didymium iridis is located on a linear, multi-copy, non-Mendelian chromosome. Efforts to determine the complete sequence by short-read sequencing technologies have been prevented by the presence of highly …
Read PDFOxford nanopore sequencing enabled real-time, long-read analysis of DNA by detecting ionic current signals associated with K-mer sequences. Although many studies analyzed sequence and modification detection, our understanding of how multiple nucleotides of the K-mer …
Read PDFPterocryptis cochinchinensis is a small freshwater catfish distributed across the Southeast Asia and southern China. It plays an important role in maintaining inland aquatic biodiversity and serves as a valuable model for phylogeographic research. However, …
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