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Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called …
Read PDFStructural and repeat variation relevant to autism has remained largely inaccessible to short-read sequencing. Using long-read genome sequencing, a recent study reveals previously hidden variants at scale, quantifies their contribution to autism risk, and links …
Read PDF<h4>Background</h4>Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when …
Read PDF<i>Drosophila melanogaster</i> is a powerful model system to study histone gene regulation. However, <i>D. melanogaster</i> histone coding sequences are nearly identical, constraining use of this model in elucidating the regulation of individual members of this …
Read PDF<i>Dugesia japonica</i> is an excellent animal model for studying the regeneration mechanism due to its characteristics of rapid regeneration and easy breeding. PacBio sequencing was performed on the intact planarians (In) and regenerating planarians of …
Read PDF<h4>Background</h4>Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos …
Read PDFThe Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a …
Read PDFStrawberry (<i>Fragaria</i> x <i>ananassa</i>) is an allopolyploid species with diverse and complex transcripts. The regulatory mechanisms of fruit development and maturation have been extensively studied; however, little is known about the signaling mechanisms that direct …
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Read PDF<h4>Background</h4>Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding …
Read PDFAntimicrobial resistance (AMR) is a major public health threat. Plasmids are able to transfer AMR genes among bacterial isolates. Whole genome sequencing (WGS) is a powerful tool to monitor AMR determinants. However, plasmids are difficult …
Read PDFPoplars are worldwidely cultivated with ecologically and economically important value. <i>Populus alba</i> var. <i>pyramidalis</i> (= <i>P</i>. <i>bolleana</i>) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to …
Read PDFRNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We developed a new approach to address this challenge, …
Read PDFWhole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such …
Read PDFTrifoliate yam (<i>Dioscorea dumetorum</i>) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 h after harvesting and renders the tubers inedible. Genomic resources …
Read PDFAntigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded …
Read PDFAlthough shrimp are of great economic importance, few full-length shrimp transcriptomes are available. Here, we used Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology to generate transcripts from the Pacific white shrimp (Litopenaeus vannamei). We …
Read PDFStructural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies …
Read PDF<h4>Background</h4>Whole mitogenomes or short fragments (i.e., 300-700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' …
Read PDFWith the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning …
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