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

TY - JOUR

T1 - A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

AU - Zhang, Runxuan

AU - Calixto, Cristiane P. G.

AU - Marquez, Yamile

AU - Venhuizen, Peter

AU - Tzioutziou, Nikoleta A.

AU - Guo, Wenbin

AU - Spensley, Mark

AU - Entizne, Juan Carlos

AU - Lewandowska, Dominika

AU - ten Have, Sara

AU - Frei dit Frey, Nicolas

AU - Hirt, Heribert

AU - James, Allan B.

AU - Nimmo, Hugh G.

AU - Barta, Andrea

AU - Kalyna, Maria

AU - Brown, John W. S.

N1 - BBSRC grants: BB/K013661/1 and BB/K006568/1.

PY - 2017/5/19

Y1 - 2017/5/19

N2 - 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.

AB - 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.

KW - RNA-seq

KW - Alternative splicing

KW - Arabidopsis thaliana

KW - Transcript quantification

KW - Transcript assembly

UR - https://www.biorxiv.org/content/10.1101/051938v1

UR - https://www.scopus.com/pages/publications/85026999986

U2 - 10.1093/nar/gkx267

DO - 10.1093/nar/gkx267

M3 - Article

C2 - 28402429

SN - 0305-1048

VL - 45

SP - 5061

EP - 5073

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 9

ER -