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The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo …
Read PDFIn August 2025, Mozambique's Central Veterinary Laboratory, part of the Agricultural Research Institute, received broiler chicken carcasses for investigation after reports of elevated flock mortality. Pooled samples from the carcasses (i.e. trachea and lung) tested …
Read PDFLong-read RNA sequencing is a powerful technology for transcriptomics, but low throughput and high cost pose challenges. Adaptive sampling, a feature of Oxford Nanopore Technologies, offers real-time enrichment by selectively ejecting non-target molecules. We evaluate …
Read PDFRecovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford …
Read PDFWe report a draft genome of a species from the ascomycotal fungal genus <i>Pseudopithomyces</i> (isolate name SBW1) obtained using a culture isolate from brewery wastewater. The 43 contig genome has a length of 39.65 Mbp, …
Read PDF<h4>Background</h4>Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target …
Read PDF<h4>Background</h4>Complex cases of retinoblastoma (RB) often require integrative molecular approaches to define tumor etiology and guide clinical management.<h4>Purpose</h4>Our aim was to evaluate the usefulness of combining aqueous humor (AH)/plasma cell-free DNA next-generation sequencing (cfDNA-NGS) and …
Read PDFSelective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of …
Read PDFWe report complete genomes of four strains of <i>Ochrobactrum pituitosum</i> and three strains of <i>Pseudochrobactrum saccharolyticum</i> isolated from gut microbiomes of <i>Caenorhabditis elegans</i> colonized with microbial communities extracted from garden compost. Genomes were assembled from …
Read PDF<h4>Background</h4>Donor-derived cell-free DNA (ddcfDNA) has been shown to be useful in monitoring lung graft health, and single nucleotide variations (SNVs) between donor and recipient are used to identify ddcfDNA in post-transplant recipient blood. One limitation …
Read PDFBacterial culture collections represent a valuable tool for mechanistic understanding of microbiome assemblies and are increasingly used to assemble tailored synthetic communities to characterize their microbe-microbe interactions and those with the environment. Given the size …
Read PDFThe D4Z4 locus is a macrosatellite array on Chromosome 4q normally comprising 8 to >100 3.3-kb repeat units. Its size and repetitiveness render it refractory to most sequencing technologies; consequently, its genetic and epigenetic architectures …
Read PDFPelodiscus sinensis (Chinese soft-shelled turtle) is a freshwater species with economic and biomedical value. Here, we report a near-telomere-to-telomere (near-T2T) chromosome-level genome assembly. Using a combination of PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C …
Read PDFSweetpotato is a key crop for global food security, particularly in Burkina Faso, where its productivity is increasingly threatened by viral diseases, especially those caused by CRESS-DNA viruses. However, the diversity of these viruses in …
Read PDFThis study aimed to analyse the microbiome of chronic infected diabetic foot ulcers (DFUs) using parallel methods: traditional culture (the culturome), 16S rRNA gene sequencing (the microbiome) as well as the Antibiotic Resistance Gene (ARG) …
Read PDFArtemisinin-based combination therapies (ACTs) remain the cornerstone of malaria treatment in Rwanda, but the emergence of drug resistance threatens their efficacy. This study conducted genomic surveillance of <i>Plasmodium falciparum</i> isolates collected in Kigali between October …
Read PDF<h4>Background</h4>Molecular typing of Mycobacterium tuberculosis complex isolates enhances understanding of tuberculosis (TB) transmission dynamics, supporting public health efforts in outbreak investigations. This study aims to validate TBpore, a novel bioinformatic pipeline for clustering TB transmission …
Read PDF<i>Limosilactobacillus reuteri</i>, formerly <i>Lactobacillus reuteri</i>, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of <i>L. reuteri</i> strain HDB from the stool of …
Read PDFFlow velocity is a key environmental factor that exerts multifaceted effects on fish growth and adaptation. Through long-term natural selection, fish have evolved adaptability to specific flow conditions, which not only relate to oxygen supply …
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