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

Runxuan Zhang, Cristiane P. G. Calixto, Yamile Marquez, Peter Venhuizen, Nikoleta A. Tzioutziou, Wenbin Guo, Mark Spensley, Juan Carlos Entizne, Dominika Lewandowska, Sara ten Have, Nicolas Frei dit Frey, Heribert Hirt, Allan B. James, Hugh G. Nimmo, Andrea Barta, Maria Kalyna, John W. S. Brown (Lead / Corresponding author)

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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.
Original languageEnglish
Pages (from-to)5061-5073
Number of pages13
JournalNucleic Acids Research
Volume45
Issue number9
Early online date11 Apr 2017
DOIs
Publication statusPublished - 19 May 2017

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Keywords

  • RNA-seq
  • Alternative splicing
  • Arabidopsis thaliana
  • Transcript quantification
  • Transcript assembly

Cite this

Zhang, R., Calixto, C. P. G., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Entizne, J. C., Lewandowska, D., ten Have, S., Frei dit Frey, N., Hirt, H., James, A. B., Nimmo, H. G., Barta, A., Kalyna, M., & Brown, J. W. S. (2017). A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research, 45(9), 5061-5073. https://doi.org/10.1093/nar/gkx267