Genome-wide landscape of alternative splicing events in brachypodium distachyon
Autor: | Gaurav Sablok, Gengkon Lum, Braden Walters, Xiang Jia Min |
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Rok vydání: | 2013 |
Předmět: |
functional ontology
Settore BIO/18 - GENETICA Plant Biology & Botany Genes Plant intron retention Evolution Molecular Exon Genetics Molecular Biology Gene Expressed Sequence Tags Expressed sequence tag Brachypodium distachyon biology Alternative splicing Intron food and beverages General Medicine Genomics Exons Full Papers biology.organism_classification Introns Alternative Splicing RNA splicing Brachypodium Genome Plant |
Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
Popis: | 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 ~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/). © The Author 2012. |
Databáze: | OpenAIRE |
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