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.