A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
Calixto, Cristiane P. G.
Tzioutziou, Nikoleta A.
Entizne, Juan Carlos
ten Have, Sara
Frei dit Frey, Nicolas
James, Allan B.
Nimmo, Hugh G.
Brown, John W. S.
KAUST DepartmentBiological and Environmental Science and Engineering (BESE) Division
Center for Desert Agriculture
Plant Science Program
Online Publication Date2017-04-11
Print Publication Date2017-05-19
Permanent link to this recordhttp://hdl.handle.net/10754/623319
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AbstractAlternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
CitationZhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, et al. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research. Available: http://dx.doi.org/10.1093/nar/gkx267.
SponsorsBiotechnology and Biological Sciences Research Council (BBSRC) [BB/K013661/1 and BB/K006568/1 to J.B.; BB/K006835/1 to H.N.]; Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to J.B. and R.Z.]; Austrian Science Fund (FWF) [P26333 to M.K., DK W1207 to A.B.]; LABEX Saclay Plant Sciences [to H.H.]; BBSRC EASTBIO PhD studentships (to N.T. and J.C.); European Alternative Splicing Network of Excellence (EURASNET) [LSHG-CT-2005-518238] for catalyzing important collaborations. Funding for open access charge: University of Dundee.
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
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