Single-nucleotide resolution mapping of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns
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 154,368 splice junctions with 16,437 AS events in 10,197 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 (TE) were found in only 2.9% of all G. raimondii introns, they are present in 43% of the retained introns, suggest that TE insertion may be an important mechanism for intron retention during AS. Majority of the TE insertions are concentrated 040 nt upstream of the 3'-splice site, substantially altering the distribution of branch points from preferred positions and reduces 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 vertebrate and higher plant.
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