Genome-wide landscape of alternative splicing events in brachypodium distachyon

Walters, B; Lum, G; Sablok, G; Min, XJ

Genome-wide landscape of alternative splicing events in brachypodium distachyon

Walters, B Lum, G Sablok, G

Min, XJ

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Publication Type:: Journal Article
Citation:: DNA Research, 2013, 20 (2), pp. 163 - 171
Issue Date:: 2013-04-01

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Field	Value	Language
dc.contributor.author	Walters, B	en_US
dc.contributor.author	Lum, G	en_US
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Min, XJ	en_US
dc.date.issued	2013-04-01	en_US
dc.identifier.citation	DNA Research, 2013, 20 (2), pp. 163 - 171	en_US
dc.identifier.issn	1340-2838	en_US
dc.identifier.uri	http://hdl.handle.net/10453/33830
dc.description.abstract	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.	en_US
dc.relation.ispartof	DNA Research	en_US
dc.relation.isbasedon	10.1093/dnares/dss041	en_US
dc.subject.classification	Plant Biology & Botany	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Alternative Splicing	en_US
dc.subject.mesh	Genes, Plant	en_US
dc.subject.mesh	Genome, Plant	en_US
dc.subject.mesh	Introns	en_US
dc.subject.mesh	Exons	en_US
dc.subject.mesh	Expressed Sequence Tags	en_US
dc.subject.mesh	Brachypodium	en_US
dc.title	Genome-wide landscape of alternative splicing events in brachypodium distachyon	en_US
dc.type	Journal Article
utslib.citation.volume	2	en_US
utslib.citation.volume	20	en_US
utslib.for	0604 Genetics	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.issue	2	en_US
pubs.publication-status	Published	en_US
pubs.volume	20	en_US

Abstract:

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.

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http://hdl.handle.net/10453/33830