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Magnolia zenii (Magnoliaceae) is an extremely endangered tree species endemic to eastern China, has only 115 individuals remaining in the wild. By integrating PacBio HiFi (49×), Oxford Nanopore (ONT; 101×) long-read sequencing, and Hi-C chromatin …
Read PDFShort tandem repeats (STRs) are repetitive DNA sequences that contribute to genetic diversity and play a significant role in disease susceptibility. The human genome contains approximately 1.5 million STR loci, collectively covering around 3% of …
Read PDFSomatic structural variations (SVs) are critical in cancer genomes, yet their detection from long-read sequencing remains challenging due to alignment errors in repetitive regions. We develop SVScope, leveraging full-length reads and local graph-genome optimization with …
Read PDFAmplicon sequencing is a popular method for understanding the diversity of bacterial communities in samples containing multiple organisms as exemplified by 16S rRNA sequencing. Another application of amplicon sequencing includes multiplexing both primer sets and …
Read PDFMobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike …
Read PDFLower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation …
Read PDFAs the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand …
Read PDF<h4>Summary</h4>Long-read DNA sequencing is increasingly applied for whole-genome studies, yet experimental planning often lacks reliable estimates of target region coverage, leading to costly and time-consuming pilot studies and replicates. We present esloco, a Monte Carlo-based …
Read PDFWe present a DNA extraction protocol for atmospheric bioaerosol samples collected on glass-fiber filters widely used in air quality monitoring. The protocol produces high-quality molecules suitable for third-generation sequencing and other applications. The initial protocol …
Read PDFAffordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infections or emerging …
Read PDFThe main agent of Lyme borreliosis (LB) in North America, the bacteria <i>Borrelia burgdorferi</i>, is spreading in Canada following the northward expansion of its primary tick vectors, <i>Ixodes scapularis</i> and <i>Ixodes pacificus</i>. Despite the importance …
Read PDFHistorically, antibiotic development has been driven by research into secondary metabolism which is responsible for the biosynthesis of so-called natural products. This research has been revolutionized by our growing capacity to rapidly generate and analyze …
Read PDF<h4>Background</h4>Bacterial genome exploration and outbreak analysis rely heavily on robust whole-genome sequencing and bioinformatics analysis. Widely-used genomic methods, such as genotyping and detection of genetic markers demand high sequencing accuracy and precise genome assembly for …
Read PDF<h4>Background</h4>Structural variants (SVs) are increasingly recognized as key contributors to human diseases. However, our understanding of SVs in health and disease is limited, mainly due to their structural complexity and variable length in individuals, as …
Read PDF<b>Background/Objectives</b>: Intra-abdominal infections (IAIs) constitute significant clinical challenges that can rapidly progress to life-threatening conditions if not promptly diagnosed and treated. Traditional pathogen identification methodologies, predominantly culture-based, frequently necessitate extended turnaround times (TATs) and exhibit …
Read PDFRestriction-modification (RM) systems contribute to genome plasticity in <i>Mycoplasma hominis</i>, a facultative pathogen with an extremely small but highly heterogeneous genome. The <i>Mho</i>VII RM system, which contains a fusion of two methyltransferases (MTases), M1 and …
Read PDFThe mass rearing of insects for food and feed is increasing significantly, but it presents challenges in detecting and characterizing pathogens which may cause severe economic losses. Much attention is placed on detecting viruses, bacteria …
Read PDF<h4>Background</h4>Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet …
Read PDF<h4>Motivation</h4>Single-molecule assays like NOMe-seq, dSMF, and Nanopore are superior to DNase-seq and ATAC-seq as they do not destroy DNA. Thus, they enable quantification of all three, that is, protein-free, Transcription Factor-bound, and histone-complex-bound states. But …
Read PDFPseudomonas syringae complex (Psc) causes bacterial blight and canker on blueberry and other fruit crops. Reliable and cost-effective pathogen detection is essential for managing crop diseases. The Oxford Nanopore MinION has emerged as a powerful …
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