A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Handle URI:
http://hdl.handle.net/10754/623319
Title:
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
Authors:
Zhang, Runxuan; Calixto, Cristiane P. G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten Have, Sara; Frei dit Frey, Nicolas; Hirt, Heribert ( 0000-0003-3119-9633 ) ; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria ( 0000-0003-4702-7625 ) ; Brown, John W. S. ( 0000-0003-2979-779X )
Abstract:
Alternative 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.
KAUST Department:
Center for Desert Agriculture
Citation:
Zhang 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.
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
5-Apr-2017
DOI:
10.1093/nar/gkx267
Type:
Article
ISSN:
0305-1048; 1362-4962
Sponsors:
Biotechnology 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.
Additional Links:
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx267
Appears in Collections:
Articles; Center for Desert Agriculture

Full metadata record

DC FieldValue Language
dc.contributor.authorZhang, Runxuanen
dc.contributor.authorCalixto, Cristiane P. G.en
dc.contributor.authorMarquez, Yamileen
dc.contributor.authorVenhuizen, Peteren
dc.contributor.authorTzioutziou, Nikoleta A.en
dc.contributor.authorGuo, Wenbinen
dc.contributor.authorSpensley, Marken
dc.contributor.authorEntizne, Juan Carlosen
dc.contributor.authorLewandowska, Dominikaen
dc.contributor.authorten Have, Saraen
dc.contributor.authorFrei dit Frey, Nicolasen
dc.contributor.authorHirt, Heriberten
dc.contributor.authorJames, Allan B.en
dc.contributor.authorNimmo, Hugh G.en
dc.contributor.authorBarta, Andreaen
dc.contributor.authorKalyna, Mariaen
dc.contributor.authorBrown, John W. S.en
dc.date.accessioned2017-05-04T06:39:20Z-
dc.date.available2017-05-04T06:39:20Z-
dc.date.issued2017-04-05en
dc.identifier.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.en
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkx267en
dc.identifier.urihttp://hdl.handle.net/10754/623319-
dc.description.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.en
dc.description.sponsorshipBiotechnology 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.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx267en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleA high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicingen
dc.typeArticleen
dc.contributor.departmentCenter for Desert Agricultureen
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInformatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UKen
dc.contributor.institutionPlant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UKen
dc.contributor.institutionMax F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austriaen
dc.contributor.institutionEMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spainen
dc.contributor.institutionThe Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canadaen
dc.contributor.institutionCell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UKen
dc.contributor.institutionCentre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UKen
dc.contributor.institutionInstitute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, Franceen
dc.contributor.institutionLaboratoire de Recherche en Sciences V´eg´etales, UMR5546, Universit´e Toulouse 3, CNRS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, Franceen
dc.contributor.institutionInstitute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UKen
dc.contributor.institutionDepartment of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austriaen
kaust.authorHirt, Heriberten
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