title: Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns.
abstract: Alternative splicing (AS) is a vital genetic mechanism that enhances the diversity of eukaryotic transcriptomes. Here, we generated 8.3 Gb high-quality RNA-sequencing data from cotton (Gossypium raimondii) and performed a systematic, comparative analysis of AS events. We mapped 85% of the RNA-sequencing data onto the reference genome and identified 154368 splice junctions with 16437 as events in 10197 genes. Intron retention constituted the majority (40%) of all AS events in G. raimondii. Comparison across 11 eukaryote species showed that intron retention is the most common AS type in higher plants. Although transposable elements (TEs) were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggesting that TE-insertion may be an important mechanism for intron retention during AS. The majority of the TE insertions are concentrated 0-40 nt upstream of the 3'-splice site, substantially altering the distribution of branch points from preferred positions and reducing the efficiency of intron splicing by decreasing RNA secondary structure flexibility. Our data suggest that TE-insertion-induced changes in branch point-site distribution are important for intron retention-type AS. Our findings may help explain the vast differences in intron-retention frequencies between vertebrates and higher plants.
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Li
authors.forename: Guanghui
authors.initials: G
authors.lastname: Xiao
authors.forename: Yu-Xian
authors.initials: YX
authors.lastname: Zhu
mesh_terms: D017398:Alternative Splicing; D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling; D023281:Genomics; D003368:Gossypium / Q000235:genetics*; D007438:Introns / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D004251:DNA Transposable Elements; D009711:Nucleotides
keywords: RNA-seq; alternative splicing; cotton; intron retention.; transposable element