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dc.contributor.authorZhang, Runxuan
dc.contributor.authorCalixto, Cristiane P G
dc.contributor.authorMarquez, Yamile
dc.contributor.authorVenhuizen, Peter
dc.contributor.authorTzioutziou, Nikoleta A
dc.contributor.authorGuo, Wenbin
dc.contributor.authorSpensley, Mark
dc.contributor.authorFrei dit Frey, Nicolas
dc.contributor.authorHirt, Heribert
dc.contributor.authorJames, Allan B
dc.contributor.authorNimmo, Hugh G
dc.contributor.authorBarta, Andrea
dc.contributor.authorKalyna, Maria
dc.contributor.authorBrown, John W S
dc.date.accessioned2016-08-10T12:41:33Z
dc.date.available2016-08-10T12:41:33Z
dc.date.issued2016-05-06
dc.identifier.doi10.1101/051938
dc.identifier.urihttp://hdl.handle.net/10754/618217
dc.description.abstractBackground Alternative splicing is the major post-transcriptional mechanism by which gene expression is regulated and affects a wide range of processes and responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification of individual transcript isoforms to identify changes in expression and alternative splicing. RNA-seq is an essential modern tool but its ability to accurately quantify transcript isoforms depends on the diversity, completeness and quality of the transcript information. Results We have developed a new Reference Transcript Dataset for Arabidopsis (AtRTD2) for RNA-seq analysis containing over 82k non-redundant transcripts, whereby 74,194 transcripts originate from 27,667 protein-coding genes. A total of 13,524 protein-coding genes have at least one alternatively spliced transcript in AtRTD2 such that about 60% of the 22,453 protein-coding, intron-containing genes in Arabidopsis undergo alternative splicing. More than 600 putative U12 introns were identified in more than 2,000 transcripts. AtRTD2 was generated from transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD, and Araport11 transcript assemblies. AtRTD2 increases the diversity of transcripts and through application of stringent filters represents the most extensive and accurate transcript collection for Arabidopsis to date. We have demonstrated a generally good correlation of alternative splicing ratios from RNA-seq data analysed by Salmon and experimental data from high resolution RT-PCR. However, we have observed inaccurate quantification of transcript isoforms for genes with multiple transcripts which have variation in the lengths of their UTRs. This variation is not effectively corrected in RNA-seq analysis programmes and will therefore impact RNA-seq analyses generally. To address this, we have tested different genome-wide modifications of AtRTD2 to improve transcript quantification and alternative splicing analysis. As a result, we release AtRTD2-QUASI specifically for use in Quantification of Alternatively Spliced Isoforms and demonstrate that it out-performs other available transcriptomes for RNA-seq analysis. Conclusions We have generated a new transcriptome resource for RNA-seq analyses in Arabidopsis (AtRTD2) designed to address quantification of different isoforms and alternative splicing in gene expression studies. Experimental validation of alternative splicing changes identified inaccuracies in transcript quantification due to UTR length variation. To solve this problem, we also release a modified reference transcriptome, AtRTD2-QUASI for quantification of transcript isoforms, which shows high correlation with experimental data.
dc.description.sponsorshipWe thank Janet Laird (University of Glasgow) and Linda Milne, Micha Bayer and Iain Milne (James Hutton Institute) for technical assistance.
dc.language.isoen
dc.publisherCold Spring Harbor Laboratory Press
dc.relation.urlhttp://biorxiv.org/content/early/2016/05/06/051938
dc.rightsThe copyright holder for this preprint is the author/funder. It is made available under a CC-BY-ND 4.0 International license. http://creativecommons.org/licenses/by-nd/4.0/
dc.titleAtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentPlant Science Program
dc.contributor.departmentDesert Agriculture Initiative
dc.eprint.versionPre-print
dc.contributor.institutionInformatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
dc.contributor.institutionPlant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, Scotland, UK
dc.contributor.institutionMax F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030, Vienna, Austria
dc.contributor.institutionThe Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada
dc.contributor.institutionInstitute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France
dc.contributor.institutionInstitute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland
dc.contributor.institutionDepartment of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria
dc.contributor.institutionCell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
dc.contributor.institutionEMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain
dc.contributor.institutionLaboratoire de Recherche en Sciences Végétales, UMR5546, University of Toulouse 3, CNRS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet-Tolosan, France.
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personHirt, Heribert
refterms.dateFOA2018-06-13T12:47:21Z


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