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Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome …
Read PDFMicroplitis pallidipes Szépligeti (Hymenoptera: Braconidae) is an important parasitic wasp of second and third-instar noctuid larvae such as the insect pests Spodoptera exigua, Spodoptera litura, and Spodoptera frugiperda. As in other insects, M. pallidipes has …
Read PDF<h4>Background</h4>Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced …
Read PDFDNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the …
Read PDFThe common cutworm (CCW, <i>Spodopteraab litura</i> Fabricius) is one of the pests that most severely infect soybean (<i>Glycine max</i> L. Merr.). In a previous report, quantitative trait loci (QTL) analysis of CCW resistance using a …
Read PDFKaryotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result …
Read PDFSingle-molecule long-read sequencing datasets were generated for a son-father-mother trio of Han Chinese descent that is part of the Genome in a Bottle (GIAB) consortium portfolio. The dataset was generated using the Pacific Biosciences Sequel …
Read PDFLong-read sequencing (LRS) has become increasingly important in RNA research due to its strength in resolving complex transcriptomic architectures. In this regard, currently two LRS platforms have demonstrated adequate performance: the Single Molecule Real-Time Sequencing …
Read PDF<h4>Background</h4>Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them …
Read PDF<h4>Summary</h4>Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.<h4>Availability and implementation</h4>The NanoPack tools are written in Python3 and released under …
Read PDFWe used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and …
Read PDFOver the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. …
Read PDFIllumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined …
Read PDFSystematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these …
Read PDFLong-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed …
Read PDFRecently developed nanopore sequencing technologies offer a unique opportunity to rapidly close the genome and to identify complete sequences of mobile genetic elements (MGEs). In this study, 17 isolates of <i>Listeria monocytogenes</i> (<i>Lm</i>) epidemic clone …
Read PDFHybrid genome assembly has emerged as an important technique in bacterial genomics, but cost and labor requirements limit large-scale application. We present Ultraplexing, a method to improve per-sample sequencing cost and hands-on time of Nanopore …
Read PDFBrucellaphage EF4 was isolated from elk feces. The 38,321-bp double-stranded DNA genome is predicted to contain 72 coding regions, 38 of which have been assigned predicted functions. This phage displays nucleotide similarity to other brucellaphages …
Read PDFGenomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies. In particular, balanced translocations and inversions can neither be identified by microarrays since they do …
Read PDFTransgene insertion patterns are critical for the analysis of transgenic animals because the influence of transgenes may change depending on the insertion pattern (such as copy numbers and orientations of concatenations) and the insertion position …
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