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Variant phasing and haplotypic expression from long-read sequencing in maize
Haplotype phasing maize genetic variants is important for genome interpretation, population genetic analysis and functional analysis of allelic activity. We performed an isoform-level phasing study using two maize inbred lines and their reciprocal crosses, based …
Read PDFLong-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue
Adherent-invasive Escherichia coli (AIEC) is a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn's disease, and colorectal cancer. AIEC are genetically diverse, and in the absence of a universal molecular signature, are defined by …
Read PDFEvaluating Structural Variation Detection Tools for Long-Read Sequencing Datasets in <i>Saccharomyces cerevisiae</i>
Structural variation (SV) represents a major form of genetic variations that contribute to polymorphic variations, human diseases, and phenotypes in many organisms. Long-read sequencing has been successfully used to identify novel and complex SVs. However, …
Read PDFThe Single-molecule long-read sequencing of Scylla paramamosain
Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different …
Read PDFHigh-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing
The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. Here we utilize a low-cell number transcriptome based on the Smart-seq2 method to perform long-read sequencing. …
Read PDFClassification of Changes in the Fecal Microbiota Associated with Colonic Adenomatous Polyps Using a Long-Read Sequencing Platform
The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological impacts on the organism it inhabits. A growing body …
Read PDFImproved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing
<h4>Purpose</h4>Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility …
Read PDFAmplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
<h4>Background</h4>One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging. Here, we present SMRT-OTS and Nano-OTS, two novel, …
Read PDFMicrobial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing
<h4>Objective</h4>Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this …
Read PDFLeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology
Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that …
Read PDFCombined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce …
Read PDFAnalysis of a small outbreak of Shiga toxin-producing <i>Escherichia coli</i> O157:H7 using long-read sequencing
Compared to short-read sequencing data, long-read sequencing facilitates single contiguous <i>de novo</i> assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing …
Read PDFLong-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)
<h4>Background</h4>Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters.<h4>Results</h4>In this study, we …
Read PDFNanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs using …
Read PDFLong-fragment targeted capture for long-read sequencing of plastomes
<h4>Premise</h4>Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization …
Read PDFTime-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach
<h4>Objective</h4>In this study, we applied two long-read sequencing (LRS) approaches, including single-molecule real-time and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of host gene expression as a response to Vaccinia virus infection. Transcriptomes …
Read PDFLong-Read Sequencing Emerging in Medical Genetics
The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing …
Read PDFLong-Read Sequencing to Unravel Complex Structural Variants of <i>CEP78</i> Leading to Cone-Rod Dystrophy and Hearing Loss
Inactivating variants as well as a missense variant in the centrosomal <i>CEP78</i> gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. …
Read PDFSingle-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L
Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value. However, a full-length R. lapponicum transcriptome is still lacking. In the present study, we used the Pacific Biosciences single-molecule real-time …
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