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<h4>Background</h4>Structural variants (SVs) play a crucial role in gene regulation, trait association, and disease in humans. SV genotyping has been extensively applied in genomics research and clinical diagnosis. Although a growing number of SV genotyping …
Read PDFFollicle selection is an important step in the laying process of chicken, which is closely related to the laying performance and fecundity of hens. Follicle selection mainly depends on the regulation of follicle-stimulating hormone (FSH) …
Read PDFDespite the successful identification of causative genes and genetic variants of retinitis pigmentosa (RP), many patients have not been molecularly diagnosed. Our recent study using targeted short-read sequencing showed that the proportion of carriers of …
Read PDFHuntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by CAG trinucleotide repeat expansions in exon-1 of <i>huntingtin</i> (<i>HTT</i>). Currently, there is no cure for HD, and the clinical care of individuals with HD …
Read PDF<h4>Background</h4>Thalassemia is a common inherited hemoglobin disorder caused by a deficiency of one or more globin subunits. Substitution variants and deletions in the <i>HBB</i> gene are the major causes of β-thalassemia, of which large fragment …
Read PDFThe majority of released rye cultivars are susceptible to leaf rust because of a low level of resistance in the predominant hybrid rye-breeding gene pools Petkus and Carsten. To discover new sources of leaf rust …
Read PDFTransposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions …
Read PDFLong-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T …
Read PDF<h4>Background</h4>The filaggrin (FLG) protein, encoded by the FLG gene, is an intermediate filament-associated protein that plays a crucial role in the terminal stages of human epidermal differentiation. Loss-of-function mutations in the FLG exon 3 have …
Read PDFThe complete sequencing of human centromeres, which are filled with highly repetitive elements, has long been challenging. In human centromeres, α-satellite monomers of about 171 bp in length are the basic repeating units, but α-satellite …
Read PDFThe use of pharmacogenomics in clinical practice is becoming standard of care. However, due to the complex genetic makeup of pharmacogenes, not all genetic variation is currently accounted for. Here, we show the utility of …
Read PDFArthrospira platensis is a filamentous cyanobacterium that is cultivated and used worldwide as a source of food and food additives. Here, we report the complete genome sequence (6,818,916 bp) of A. platensis NIES-39, one of …
Read PDFThe complete genome sequences of Rouxiella badensis DSM 100043<sup>T</sup> and Rouxiella chamberiensis DSM 28324<sup>T</sup> were determined using Oxford Nanopore long-read sequencing and the Flye assembler. The former contains a circular chromosome of 4,964,479 bp and …
Read PDFAlternative polyadenylation (APA) is widespread among metazoans and has been shown to have important impacts on mRNA stability and protein expression. Beyond a handful of well-studied organisms, however, its existence and consequences have not been …
Read PDFNeurodegenerative diseases exhibit chronic progressive lesions in the central and peripheral nervous systems with unclear causes. The search for pathogenic mutations in human neurodegenerative diseases has benefited from massively parallel short-read sequencers. However, genomic regions, …
Read PDFWhole-genome sequencing is widely used to better understand the transmission dynamics, the evolution and the emergence of new variants of viral pathogens. This can bring crucial information to stakeholders for disease management. Unfortunately, aquatic virus …
Read PDF<h4>Background</h4>Transmissible viral proventriculitis (TVP) causes significant economic loss to the poultry industry. However, the exact causative agents are obscure. Here we examine the virome of proventriculus from specified pathogen free (SPF) chickens that reproduced by …
Read PDFGBA variants carriers are at increased risk of Parkinson's disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to structural variants, complicating genetic analysis. We present two methods to resolve recombinant …
Read PDFSequencing high molecular weight (HMW) DNA with long-read and linked-read technologies has promoted a major increase in more complete genome sequences for nonmodel organisms. Sequencing approaches that rely on HMW DNA have been limited to …
Read PDFStructural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by …
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