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Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) introduce substantial inaccuracies, complicating downstream applications such as transcript annotation and gene fusion detection. Current basecalling models are unable to detect or mitigate these artifacts, limiting the …
Read PDF<h4>Background/objectives</h4>Since its emergence in late 2019, SARS-CoV-2 has demonstrated remarkable genetic diversity driven by mutations and recombination events that shaped the course of the COVID-19 pandemic. Continuous genomic monitoring is essential to track viral evolution, …
Read PDFThree <i>Salmonella enterica</i> isolates were isolated from a municipal wastewater treatment plant in Knoxville, TN, USA. Genomic DNA was extracted and sequenced on the Illumina and Oxford Nanopore platforms. Annotated hybrid assemblies showed the strains …
Read PDFWe report the complete genome sequence of <i>Leucobacter</i> sp. WKLB1, an Actinobacteria isolated from the pegmatite surface in the fourth ore body in the Wagu-Kannon mine, Fukushima Prefecture. The complete circular genome has a genome …
Read PDF<h4>Background</h4>Rapid and accurate detection of drug-resistant tuberculosis (DR-TB) is crucial for ensuring effective treatment, halting transmission and preventing the amplification of resistance. Comparative evaluations of molecular diagnostic assays in high-burden settings are essential for informing …
Read PDFRapid and comprehensive analysis of metagenomic data from samples associated with foodborne outbreaks is of critical importance in food safety. Equally important is the need for automated analysis pipelines that allow the rapid and effective …
Read PDFIn October 2024, a putative novel species, belonging to the genus <i>Rossellomorea</i>, designated as strain H39_3, was isolated using Luria-Bertani medium from surface water representing station H39, located on the Hindon River, in close proximity …
Read PDFBACKGROUND: Short tandem repeats (STRs) are repetitive DNA sequences with 1–6 nucleotide repeat units, exhibiting high polymorphism due to varying repeat counts. STRs are more variable than SNPs and can cause genetic disorders. With population-scale …
Read PDFThis study investigated the longitudinal dynamics of the cecal microbiome in male and female broiler chickens from hatch (d 0) to market age (d 42) using full-length 16S rRNA gene sequencing via Oxford Nanopore Technology. …
Read PDFCreeping bentgrass (Agrostis stolonifera) is a widely used cool-season turfgrass valued for its fine texture and ability to form dense, uniform turfs. However, its complex allotetraploid genome and high repetitive content have posed challenges for …
Read PDFNanopore direct RNA sequencing holds promise for advancing our understanding of the epitranscriptome. Recently, Oxford Nanopore Technologies released basecalling models capable of detecting N6-methyladenosine (m6A), inosine (I), pseudouridine (Ψ), and 5-methylcytosine (m5C). However, their performance …
Read PDFHuman embryonic stem cell (hESC) neural differentiation involves extensive APA; however, reliance on short-read sequencing in prior studies has offered only a limited view of its complexity and dynamic regulation. Here, we integrated Oxford Nanopore …
Read PDFOBJECTIVE: Onygena corvina is a non-pathogenic, saprophytic fungus that colonizes feathers, hooves, and hair, and represents a valuable source of keratin-degrading enzymes. The only genome assembly of O. corvina available to date was obtained for …
Read PDF<h4>Background</h4>The largemouth bass (Micropterus salmoides, LMB), a globally significant aquaculture species, exhibits pronounced growth dimorphism between the sexes, yet the genetic basis of its sex determination remains unresolved. While published genomes exist, gaps, misassemblies, and …
Read PDFEndophytic fungi are increasingly recognized as pivotal contributors to plant secondary metabolism, often synthesizing bioactive compounds like those produced by their hosts. We report the first complete genome sequence for <i>Pithoascus kurdistanensis</i>, a novel endophyte …
Read PDFDeep intronic FGF14 repeat expansions have been identified as a frequent genetic cause of late-onset cerebellar ataxias, explaining ≤30% of patients. Interruptions between repeats have previously been identified to impact the penetrance in other repeat …
Read PDF<i>Pediococcus pentosaceus</i> TOKAI 759m is a Gram-positive bacterium isolated from rice in Japan. Our previous study demonstrated that this strain is a promising starter culture for soy milk yogurt due to its various beneficial properties. …
Read PDFIn this comment, we re-evaluate the proposal of <i>Aeromonas oralensis</i> as a novel species by Mashzhan et al. (2025) [...].
Read PDFMetagenomic sequencing for pathogen detection has traditionally suffered from low sensitivity due to the overwhelming presence of host nucleic acids. Commercial host-depletion kits are often prohibitively expensive and limited to specific species, hindering adoption in …
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