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<h4>Background</h4>Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of …
Read PDFAccurate transcript quantification remains a central challenge, as expression levels estimated by different computational tools (e.g. Cufflinks, StringTie, featureCounts, RSEM) often exhibit substantial discrepancies. The observed variability stems from intrinsic transcriptional architectures and is termed …
Read PDFLong-read transcriptome sequencing (long-RNA-seq) revolutionizes transcriptome research by enabling full-length transcript analysis for comprehensive exploration of isoform diversity. We developed IFDlong, a probabilistic framework and software suite for detecting isoform and fusion transcripts from bulk …
Read PDFAlternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its …
Read PDFDespite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read …
Read PDFTranscriptome complexity plays crucial roles in regulating the biological functions of eukaryotes. Except for functional genes, alternative splicing and fusion transcripts produce a vast expansion of transcriptome diversity. In this study, we applied PacBio single-molecule …
Read PDFBacterial pathogens adapt rapidly to clinical and within-host selective pressures<sup>1</sup>. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation<sup>2</sup>, but their activity and consequences in contemporary clinical populations are not well characterized. …
Read PDF<h4>Background</h4>Ammopiptanthus nanus is a rare broad-leaved shrub that is found in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in …
Read PDFThe lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its …
Read PDF<h4>Background</h4>Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively …
Read PDFThis corrects the article DOI: 10.1038/sdata.2017.194.
Read PDFDiagnosing rare genetic diseases remains a major challenge despite widespread clinical testing. Long-read RNA sequencing (RNA-seq) offers a powerful approach to capturing the effects of genetic variants on the transcriptome, yet challenges with sequencing coverage, …
Read PDFAdvances in long-read single molecule sequencing have opened new possibilities for 'benchtop' whole-genome sequencing. The Oxford Nanopore Technologies MinION is a portable device that uses nanopore technology that can directly sequence DNA molecules. MinION single …
Read PDFLong-read RNA sequencing allows for the precise characterization of full-length transcripts, which makes it an indispensable tool in transcriptomics. The human cytomegalovirus (HCMV) genome has been first sequenced in 1989 and although short-read sequencing studies …
Read PDFSweet cherry (<i>Prunus avium</i>) is a popular fruit with high nutritional value and excellent flavor. Although pollen plays an important role in the double fertilization and subsequent fruit production of this species, little is known …
Read PDFPre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their …
Read PDF<h4>Background</h4>In the past two decades, bats have emerged as an important model system to study host-pathogen interactions. More recently, it has been shown that bats may also serve as a new and excellent model to …
Read PDF<h4>Background</h4>Poxviruses are large DNA viruses that infect humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. …
Read PDFPoxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune …
Read PDF<h4>Purpose</h4>To demonstrate the utility of an amplification-free long-read sequencing method to characterize the Fuchs endothelial corneal dystrophy (FECD)-associated intronic TCF4 triplet repeat (CTG18.1).<h4>Methods</h4>We applied an amplification-free method, utilizing the CRISPR/Cas9 system, in combination with PacBio …
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