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<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 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, …
Read PDFWe characterized the 4.8 Mbp genome of <i>Escherichia coli</i> H1G2, a B1 lineage isolated from the gut of Bangladesh's national fish, Hilsa (<i>Tenualosa ilisha</i>). The complete assembly reveals specialized genes for sugar metabolism and adhesion, …
Read PDF<h4>Background</h4>Targeted next-generation sequencing has emerged as a rapid solution for diagnosing drug-resistant TB (DR-TB) directly from clinical specimens. Updating the bioinformatics software component can lead to rapid improvements in diagnostic performance. We compared the diagnostic …
Read PDFPlasmids are ubiquitous tools in molecular biology which are used for a large variety of experiments within academic and commercial labs. Both new and old plasmids have to undergo sequencing-based analysis to determine whether or …
Read PDFBovine mastitis remains a major impediment to optimal dairy production. Somatic cell count (SCC) is commonly used as an indicator of mammary gland inflammation, while milk microbiota may also reflect mastitis-related changes. Here, we employed …
Read PDF<h4>Motivation</h4>Efficient data compression is crucial for reducing storage and transmission costs associated to vast volumes of nanopore raw sequencing data. Surpassing the state-of-the-art compression performance has been challenging, and all recent progress in this direction …
Read PDF<h4>Motivation</h4>Nowadays, DNA methylation in bacteria is studied mainly using single-molecule sequencing technologies like PacBio and Oxford Nanopore. In nanopore sequencing, calling of methylated positions is provided by special models implemented directly in basecallers. Prokaryotic DNA …
Read PDFBloodstream infections (BSIs) are life-threatening and require rapid, accurate pathogen characterization to guide antimicrobial therapy. Conventional culture-based diagnostics offer limited insight into the genetic basis of antimicrobial resistance (AMR) and virulence. In this study, we …
Read PDFNext Generation Sequencing is a constantly evolving technology whose applicability is increasingly expanding into the field of routine food analysis. In this context, metabarcoding has proven to be a powerful tool for detecting food fraud …
Read PDFA small cold-water teleost endemic to Northeast Asia, Hypomesus nipponensis possesses a short lifecycle, high fecundity, and rapid population growth, with extensive introductions for aquacultural purposes across East Asia. In this study, we generated a …
Read PDFThis data paper describes bacterial and fungal communities associated with the sponge <i>Chondrilla nucula</i> collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected …
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