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

作者：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; Frey Nicolas Frei Dit; Hirt Heribert; James Allan B; Nimmo Hugh G; Barta Andrea; Kalyna Maria; Brown John W S

来源：Nucleic Acids Research, 2017, 45(9): 5061-5073.

DOI：10.1093/nar/gkx267

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.

• 出版日期2017-5-19