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The complexity of potato genetics, characterised by tetrasomic inheritance, has contributed to slower genetic gain in potato compared to other major crops. Disease resistance genes, often found in large clusters of highly similar paralogs and …
Read PDFExtrachromosomal circular DNA (eccDNA) is a type of circular DNA that exists independently of chromosomes and has garnered significant attention in various fields, particularly in the context of smaller eccDNAs, which have considerable roles in …
Read PDFThe order Siluriformes, a hyperdiverse teleost clade with over 3,000 species, exemplifies adaptive radiation through significant phenotypic innovations such as aerial respiration. However, the limited availability of high-quality genomes, particularly in underrepresented families such as …
Read PDF<h4>Motivation</h4>In prokaryotic genomes, methylation is an important epigenetic modification that regulates the uptake of foreign DNA; it can also contribute to replication or virulence. We present MPore, a novel method for the database-driven detection of …
Read PDFRare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, …
Read PDFHere, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a combination of Oxford Nanopore long-read and Illumina short-read sequencing. Yarrowia lipolytica is an industrially …
Read PDFThe fourfinger threadfin (Eleutheronema tetradactylum) is a euryhaline fish distributed across the Indo-West Pacific, from the Persian Gulf to Australia. However, the lack of high-quality genomic resources has limited genomic-level studies of its evolution, conservation, …
Read PDF<h4>Motivation</h4>Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches struggle to accurately demultiplex raw nanopore signals, failing to capture …
Read PDFThe Steppe Eagle, <i>Aquila nipalensis</i> Hodgson, 1833, is a migratory, endangered raptor experiencing population declines due to habitat loss and human persecution. This study aims to construct a high-quality <i>de novo</i> nuclear genome and complete …
Read PDFRPGR (Retinitis Pigmentosa GTPase Regulator) is the main gene involved in X-linked retinitis pigmentosa (RP) and up to 28% of sporadic RP. Pathogenic variants are mostly located in its retina-specific transcript, RPGRorf15, especially in the …
Read PDF<h4>Motivation</h4>DNA methylation serves as a key biomarker in clinical diagnostics, especially in cancer detection. With methylation-specific PCR (MSP), a widely used approach, patient samples can be screened fast and efficiently for differential methylation. During MSP, …
Read PDF<h4>Background</h4>Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA …
Read PDF<h4>Background</h4>Advances in sequencing technologies continue to improve the resolution and completeness with which human genetic variation can be characterized. Short-read sequencing remains widely used due to its high base accuracy, throughput, and cost efficiency; however, …
Read PDF<h4>Background</h4>The litchi fruit borer, <i>Conopomorpha sinensis</i> (Lepidoptera: Gracillariidae), is a devastating pest affecting litchi and longan production across Asia. Although a reference mitochondrial genome (mitogenome) has been published, its utility is limited by the lack …
Read PDFThere is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents …
Read PDF<h4>Background</h4>In microbial diagnostics, whole-genome sequencing (WGS) is used to address key questions such as species identification, presence of antimicrobial resistance genes (ARGs), virulence genes, and outbreak detection. The choice of sequencing technology is crucial to …
Read PDF<h4>Motivation</h4>Unique molecular identifiers (UMIs) enable efficient error correction in amplicon sequencing but UMI-aware analysis workflows for long-read sequencing and particularly for nanopore data are still sparse. Existing approaches lack portability, real-time sequencing support, GPU acceleration, …
Read PDFAccess to genome sequences is crucial to investigate and engineer traits in plants, explore biodiversity, and support phylogenetic studies. Over the last decade, affordable sequencing devices have substantially increased the size of the genomics community …
Read PDFCell-free DNA (cfDNA) containing cancer information has become a key biomarker for cancer liquid biopsy. Current next-generation sequencing (NGS) technology for cfDNA detection often fail to capture multiomics information, such as fragmentomics, epigenetics, and genetics, …
Read PDF<h4>Background</h4>Although many individuals with dystonia present with features indicative of single-gene etiologies, obtaining definitive genetic diagnoses can be challenging.<h4>Objective</h4>We assessed the value of nanopore-based long-read sequencing (LRS) in achieving molecular clarification of dystonic syndromes.<h4>Methods</h4>From a …
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