A Survey of Alternative Splicing in Allotetraploid Cotton (<i>Gossypium hirsutum </i>L.)

Abstract

Allotetraploid cotton ( Gossypium hirsutum L.), accounting for more than 90% of cultivated cotton worldwide, provides textile fibers and seeds. Alternative splicing (AS) is a post-transcriptional process that generates more than one RNA isoforms from a single pre-mRNA transcript, increasing the diversity of functional proteins and RNAs. We surveyed the alternatively spliced genes in cotton using expressed sequence tag (EST) and mRNA sequences available in the public databases. A total of 56,080 AS events, including 41,150 (73.4%) basic events and 14,930 (26.6%) complex events were identified, which were generated from approximately 23,930 genes. Intron retention was the most frequent event, accounting for 34.8%, followed by alternative acceptor site events (18.8%) and alternative donor site events (11.8%), and exon skipping being the least frequent event (8.0%). Complex types, which are formed by more than one basic event, are accounted for 26.6%. The estimated AS rates of genes generating AS isoforms was 27.1% in cotton. Gene Ontology and protein family analysis showed that the products of alternatively spliced genes were involved in many biological processes with diverse molecular functions. The transcripts to cotton genome mapping information can be used to improve the predicted gene models in cotton. The annotation information of AS isoforms of these genes provides a basis for future investigation on the functions of these AS genes in cotton biology. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).