Journal
DNA RESEARCH
Volume 20, Issue 2, Pages 163-171Publisher
OXFORD UNIV PRESS
DOI: 10.1093/dnares/dss041
Keywords
alternative splicing; Brachypodium distachyon; expressed sequence tags; functional ontology; intron retention
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Funding
- Youngstown State University (YSU) Research Council [12-11]
- YSU
- Ohio Plant Biotechnology Consortium through Ohio State University, Ohio Agricultural Research and Development Center [2011-001]
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Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%). We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for similar to 14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
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