Alternative splicing (AS) has played a major role in defining the protein diversity, which could be linked to phenotypic alternations. It is imperative to have a comparative resolution of AS to understand the pre-mRNAs splicing diversity. In the present research, we present a comparative assessment of the AS events in four different fruit plants including apple (Malus domestica), grape (Vitis vinifera), sweet orange (Citrus sinensis), and woodland strawberry (Fragaria vesca), using spliced mapping of the expressed sequence tags and mRNA sequences. We identified a total of 2039 AS events in apple, 2454 in grape, 1425 in orange, and 631 in strawberry, respectively. In this study grape displayed the maximum number of genes (1588) associated with the splicing, followed by apple (1580), orange (1133) and strawberry (444). Transcripts mapping analysis shows that grape plant has relatively larger intron sizes than introns in other fruit species. The data provide a basis for further functional characterization of the genes undergoing AS and can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).

Number of conserved alternative splicing genes in cereal crops. (XLS 31 kb)

BACKGROUND:Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms.RESULTS:We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions.CONCLUSIONS:AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).