AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript - specific expression in Arabidopsis thaliana

Runxuan Zhang, Cristiane P. G. Calixto, Nikoleta A. Tzioutziou, Allan B. James, Craig G. Simpson, Wenbin Guo, Yamile Marquez, Maria Kalyna, Rob Patro, Eduardo Eyras, Andrea Barta, Hugh G. Nimmo, John W. S. Brown (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)
129 Downloads (Pure)

Abstract

RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.

Original languageEnglish
Pages (from-to)96-101
Number of pages6
JournalNew Phytologist
Volume208
Issue number1
Early online date25 Jun 2015
DOIs
Publication statusPublished - Oct 2015

Keywords

  • Arabidopsis thaliana
  • Alternative splicing
  • High resolution reverse transcription (HR RT)-PCR
  • RNA-sequencing (RNA-seq)
  • Sailfish
  • Salmon
  • Transcripts per million

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