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Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic, as they compete with and prevent the detection of rare RNA transcripts, obscuring their …
Read PDFMutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing …
Read PDF<h4>Summary</h4>Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat …
Read PDFLong-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in …
Read PDF<h4>Background</h4>Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. …
Read PDFThe limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene …
Read PDFLong 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 PDFGenome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read …
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 PDFMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data …
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 PDF<h4>Background</h4>The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain …
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 PDFThe damage caused by <i>Bradysia odoriphaga</i> is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of <i>B. odoriphaga</i> have been conducted because of a lack of genomic …
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 …
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