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Splicing, including alternative splicing, is a fundamental post-transcriptional mechanism in eukaryotes that generates functional proteins and transcript diversity. Canonical splicing follows well-defined rules, such as sufficient intron and exon lengths, specific splice junction orientations, consensus …
Read PDFPolyploidization contributes to the complexity of gene expression, resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of the tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by …
Read PDFIGH@ proto-oncogene translocation is a common oncogenic event in lymphoid lineage cancers such as B-ALL, lymphoma and multiple myeloma. Here, to investigate the interplay between IGH@ proto-oncogene translocation and IGH allelic exclusion, we perform long-read …
Read PDFIt is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome …
Read PDFRNA sequencing (RNA-seq) technologies enable comprehensive transcriptomic profiling, yet systematic comparisons using identical biological samples remain limited. Here, we performed a multi-faceted comparison of long-read (PacBio) and short-read (Illumina) RNA-seq using the same RNA from …
Read PDF<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 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 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 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 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 PDFHemizygous pathogenic variants in MBTPS2 located at Xp22.12 cause IFAP syndrome, which is characterized by the triad of ichthyosis, alopecia and photophobia. Here we identified a hemizygous intronic variant in MBTPS2 (NM_015884: c.970+5G>A) in a …
Read PDF<h4>Background</h4>Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very little is known …
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