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While nanopore direct RNA sequencing has substantially advanced transcriptomics, its detection of RNA modifications remains primarily focused on abundant biological base modifications. However, therapeutic RNAs employ a diverse catalog of modifications, including base, sugar, and …
Read PDF<h4>Background</h4>Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations in sequencing platforms, primer selection, and DNA quality may influence microbial diversity assessments, particularly in studies …
Read PDFOn-demand access to information encoded in nucleotides lies at the heart of DNA/RNA applications. However, contemporary methods for targeted retrieval using PCR amplification or bead-based extraction, rely on Watson-Crick base pairing and pre-defined primers, limiting …
Read PDFOBJECTIVES: Obrimoposthia wandeli is the most abundant marine planarian in the intertidal zone of the maritime Antarctic region and is presumed to have adapted to the extreme conditions of the Southern Ocean. However, genomic studies …
Read PDFLeishmania spp. regulate gene expression posttranscriptionally, yet untranslated regions (UTRs) that can affect mRNA stability and translation remain poorly delineated. We generated a de novo assembled genome for Leishmania donovani strain 1S2D (Ld1S) using PacBio …
Read PDFShrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and …
Read PDFLiverwort organellar genomes are generally highly conserved, but the subclass Pellidae (simple thalloids) shows unusual variation. This ancient yet unexplored lineage of simple thalloid liverworts provides an excellent model for investigating organellar genome evolution. In …
Read PDF<h4>Background</h4>The legume Astragalus mongholicus (A. mongholicus) has a wide variety of medicinal properties. Based on the genome of A. mongholicus, this study intended to investigate the phylogenetic position of A. mongholicus and excavate the specific …
Read PDF<h4>Background</h4>Oxford Nanopore sequencing is a long-read sequencing technology that does not rely on a polymerase to generate sequence data. Sequencing library preparation methods used in Oxford Nanopore sequencing rely on the addition of a motor …
Read PDFAvian haemosporidian parasites are vector-borne apicomplexans that infect bird species globally and pose considerable challenges in detection due to frequent co-infections and morphological convergence. In the present study, we first used Oxford Nanopore Technologies (ONT) …
Read PDFWe report whole-genome sequences of 20 <i>Bacillus cereus sensu lato</i> strains from plant-based fermentations, foodborne outbreaks, environmental sources, and dairy plants. Genomic DNA was extracted and sequenced using Oxford Nanopore Technology. These complete assemblies provide …
Read PDFLumpy Skin Disease (LSD) is a transboundary viral disease of wild and domesticated ruminants, and notifiable to the World Organisation for Animal Health (WOAH). LSD has spread rapidly in the cattle population across the African, …
Read PDF<h4>Background</h4>Cervical cancer due to high-risk human papillomavirus (HR-HPV) is the leading gynecological cancer in Sub-Saharan Africa and in the Democratic Republic of the Congo (DRC), where approximately one-quarter of people carries the sickle cell allele. …
Read PDFThe complete genome of <i>Bifidobacterium animalis</i> subsp. <i>lactis</i> BI040-a human stool isolate, was sequenced using Illumina and Oxford Nanopore technologies. The BI040 genome is composed of a circular 1,944,141-bp chromosome which carries genes potentially involved …
Read PDF<h4>Background</h4>The aim of this study was to compare microbial diversity and compositional changes under digestive stress in yogurts produced using different culture strategies in a dynamic in vitro gastrointestinal system.<h4>Methods</h4>Yogurts produced with probiotic starter cultures, …
Read PDF<h4>Background</h4>Oxford Nanopore Technologies (ONT) sequencing enables direct, long-read sequencing of DNA and RNA, preserving nucleotide modifications. During basecalling, deep neural networks translate raw nanopore signals into nucleotide sequences, internally segmenting the signal to align it …
Read PDFPetroleum pollution poses a critical environmental concern. Bioremediation has gained prominence as an eco-friendly approach for mitigating hydrocarbon pollution. This study reports the isolation and comprehensive characterization of a novel petroleum-degrading bacterium, Rhodococcus indonesiensis SARSHI1. …
Read PDF<h4>Background</h4>Sorghum bicolor and Sorghum halepense can readily hybridize, creating difficulty in identification. No genetic tools exist to accurately distinguish S. bicolor, S. halepense, and their hybrids. Detecting hybridization is essential to monitor crop-to-weed introgression. This …
Read PDFWastewater can be a useful sample to monitor disease outbreaks in the community, as it was demonstrated during the recent Severe acute respiratory syndrome coronavirus 2 pandemic. Due to housing conditions, diseases can rapidly spread …
Read PDFOxford Nanopore Technology (ONT)-based methylation sequencing is emerging as a powerful approach for the rapid and accurate classification of brain tumors, an essential component of precision oncology. However, its broader clinical adoption has been limited …
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