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

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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 | James, Allan B. | Nimmo, Hugh G. | Barta, Andrea | Kalyna, Maria | Brown, John W. S.

Edité par CCSD ; Oxford University Press -

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.

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