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Here, we develop and apply a semi-quantitative method for the high-confidence identification of pseudouridylated sites on mammalian mRNAs via direct long-read nanopore sequencing. A comparative analysis of a modification-free transcriptome reveals that the depth of …
Read PDFIntegration of human papillomavirus (HPV) DNA into the human genome is considered as a key event in cervical carcinogenesis. Here, we perform comprehensive characterization of large-range virus-human integration events in 16 HPV16-positive cervical tumors using …
Read PDFEscherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first …
Read PDF<h4>Background</h4>With the rapid development of long-read sequencing technologies, it is possible to reveal the full spectrum of genetic structural variation (SV). However, the expensive cost, finite read length and high sequencing error for long-read data …
Read PDFThe assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these …
Read PDFThe incidence of infections caused by multidrug-resistant <i>E. coli</i> strains has risen in the past years. Antibiotic resistance in <i>E. coli</i> is often mediated by acquisition and maintenance of plasmids. The study of <i>E. coli</i> …
Read PDFT cell receptors (TCRs) recognize peptide fragments presented by the major histocompatibility complex (MHC) and are critical to T cell-mediated immunity. Recent data have indicated that genetic diversity within TCR-encoding gene regions is underexplored, limiting …
Read PDF<h4>Summary</h4>Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in …
Read PDFHuman papillomavirus (HPV) is a causal agent for most cervical cancers. The physical status of the HPV genome in these cancers could be episomal, integrated, or both. HPV integration could serve as a biomarker for …
Read PDF<b>Background</b>: Thalassemia is a hereditary blood disease resulting from globin chain synthesis impairment because of α- and/or β-globin gene variants. α-thalassemia is characterized by non-deletional and deletional variants in the <i>HBA</i> gene locus, of which …
Read PDFTransposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most …
Read PDFThe concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) …
Read PDF<h4>Background</h4>Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human …
Read PDFDilated cardiomyopathy (DCM) is a common cause of heart failure (HF) and is of familial origin in 20−40% of cases. Genetic testing by next-generation sequencing (NGS) has yielded a definite diagnosis in many cases; however, …
Read PDFThe immunoglobulins (IG) or antibodies and the T cell receptors (TR) are the antigen receptors of the adaptive immune responses (AIR) of jawed vertebrates (<i>Gnathostomata</i>). IMGT<sup>®</sup>, the international ImMunoGeneTics information system<sup>®</sup>, was created in 1989 …
Read PDFMegoura crassicauda (Hemiptera: Aphididae) is a major pest species that inflicts significant damage on various legume crops worldwide, causing substantial global economic losses. In this study, we present a chromosome-scale genome assembly of M. crassicauda. …
Read PDFBacteriophage receptor-binding proteins are often attached to the tail via a conserved N-terminal adapter/anchor domain, presumed to function independently from the distal receptor-binding/catalytic domain. Using synthetic phage technology, we demonstrated that the N-terminal domain in …
Read PDFBy limiting the efficacy of selection, random drift is expected to play a major role in genome evolution. Formalizing this idea, the nearly-neutral theory predicts that the ratio of non-synonymous over synonymous polymorphism (πN/πS) within …
Read PDFThe Pacific whiteleg shrimp (Penaeus vannamei, synonym Lipopenaeus vannamei) is an important aquaculture species, and its breeding improvement relies heavily on high-quality genomic resources. Here, we sequenced the genome of the Pacific whiteleg shrimp using …
Read PDFWe present a genome assembly from a male specimen of <i>Hoplodrina octogenaria</i> (Uncertain moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 476.65 megabases. Most of the assembly (99.98%) is scaffolded …
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