Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus)

Pineapple (Ananas comosus L. Merrill) is an important tropical and subtropical fruit crop and possesses crassulacean acid metabolism (CAM) photosynthesis. Recent release of its genome sequences makes it possible to identify genes transcribed with alternatively spliced isoforms in this plant. Mapping the assembled transcripts generated by next-generation sequencing technology and existing expressed sequence tags as well as mRNA sequences to the published pineapple genome, we identified and analyzed alternative splicing (AS) events. We identified a total of 10,348 AS events involving 13,449 assembled putative unique transcripts, which were mapped to 5146 pineapple gene models that equivalent to 29.7 % of total expressed gene models. Consistent with previous findings in other plant species, intron retention (61.9 %) remains to be the dominant type among the identified AS events. Comparative genomic analysis of genes which generated pre-mRNAs having AS revealed a total of 481 genes conserved among Oryza sativa (ssp japonica), Sorghum bicolor, Zea mays, and pineapple, with 51 of them were also conserved with Brachypodium distachyon. Gene Ontology classification revealed that the products of these genes which generate AS isoforms are involved in many biological processes with diverse molecular functions. We annotated all assembled transcripts and also associated them with predicted gene models. The annotated information of these data provides a resource for further characterizing these genes and their biological roles. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).