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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
<h4>Background</h4>Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In …
Read PDFDelineation of IS<i>Ecp1</i> and IS<i>26</i>-Mediated Plasmid Fusion Processes by MinION Single-Molecule Long-Read Sequencing
We recently reported the recovery of a novel IncI1 type conjugative helper plasmid which could target mobile genetic elements (MGE) located in non-conjugative plasmid and form a fusion conjugative plasmid to mediate the horizontal transfer …
Read PDFLong-Read Sequencing Reveals Genetic Adaptation of <i>Bartonella</i> Adhesin A Among Different <i>Bartonella henselae</i> Isolates
<i>Bartonella henselae</i> is the causative agent of cat scratch disease and other clinical entities such as endocarditis and bacillary angiomatosis. The life cycle of this pathogen, with alternating host conditions, drives evolutionary and host-specific adaptations. …
Read PDFClosing Clostridium botulinum Group III Genomes Using Long-Read Sequencing
Clostridium botulinum group III is the anaerobic Gram-positive bacterium producing the deadly neurotoxin responsible for animal botulism. Here, we used long-read sequencing to produce four complete genomes from Clostridium botulinum group III neurotoxin types C, …
Read PDFUnique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing
HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression …
Read PDFLong-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma
The integration of HBV DNA into the human genome can disrupt its structure in hepatocellular carcinoma (HCC), but the complexity of HBV genomic integration remains elusive. Here we applied long-read sequencing to precisely elucidate the …
Read PDFLong-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae)
The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, …
Read PDFRe-examination of two diatom reference genomes using long-read sequencing
<h4>Background</h4>The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group. Their reference genomes, published in 2004 and 2008, respectively, were the …
Read PDFLong-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod
Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda<i>,</i> species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more …
Read PDFLong read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes
<h4>Background</h4>Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains …
Read PDFComprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in …
Read PDFLong-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in <i>Salmonella enterica</i>
<i>Salmonella enterica</i> is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on <i>Salmonella</i> isolated from retail meats and food animals. A collection of 134 …
Read PDFAnalysis of the long-read sequencing data using computational tools confirms the presence of 5-methylcytosine in the <i>Saccharomyces cerevisiae</i> genome
Modification of DNA bases plays important roles in the epigenetic regulation of eukaryotic gene expression. Among the different types of DNA methylation, 5-methylcytosine (5mC) is common in higher eukaryotes. Although bisulfite sequencing is the established …
Read PDFLong-Read Sequencing Revealed Extragenic and Intragenic Duplications of Exons 56-61 in <i>DMD</i> in an Asymptomatic Male and a DMD Patient
Expanded carrier screening (ECS) has become an increasingly common technique to assess the genetic risks of individuals in the prenatal or preconception period. Unexpected variants unrelated to referral are being increasingly detected in asymptomatic individuals …
Read PDFDetection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study
<h4>Background</h4>Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has …
Read PDFPrecise gene models using long-read sequencing reveal a unique poly(A) signal in <i>Giardia lamblia</i>
During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the …
Read PDFImproved high-throughput MHC typing for non-model species using long-read sequencing
The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host-pathogen co-evolution. …
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