title: A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
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.
authors.affiliation: Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Runxuan
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Cristiane P G
authors.initials: CPG
authors.lastname: Calixto
authors.affiliation: Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria.
authors.forename: Yamile
authors.initials: Y
authors.lastname: Marquez
authors.affiliation: Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria.
authors.forename: Peter
authors.initials: P
authors.lastname: Venhuizen
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Nikoleta A
authors.initials: NA
authors.lastname: Tzioutziou
authors.affiliation: Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.|Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Guo
authors.affiliation: The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Spensley
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Entizne
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: Dominika
authors.initials: D
authors.lastname: Lewandowska
authors.affiliation: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
authors.forename: Sara
authors.initials: S
authors.lastname: Ten Have
authors.affiliation: Institute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Frei Dit Frey
authors.affiliation: Institute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France.
authors.forename: Heribert
authors.initials: H
authors.lastname: Hirt
authors.affiliation: Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
authors.forename: Allan B
authors.initials: AB
authors.lastname: James
authors.affiliation: Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
authors.forename: Hugh G
authors.initials: HG
authors.lastname: Nimmo
authors.affiliation: Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria.
authors.forename: Andrea
authors.initials: A
authors.lastname: Barta
authors.affiliation: Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria.
authors.forename: Maria
authors.initials: M
authors.lastname: Kalyna
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.|Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
authors.forename: John W S
authors.initials: JWS
authors.lastname: Brown
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics*; D017344:Genes, Insect; D014644:Genetic Variation; D040901:Proteomics; D022661:RNA, Untranslated; D012016:Reference Values; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D022661:RNA, Untranslated