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

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.


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.

Keywords: Arabidopsis thaliana; RNA-sequencing (RNA-seq); Sailfish; Salmon; alternative splicing; high resolution reverse transcription (HR RT)-PCR; transcripts per million.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms
  • Alternative Splicing*
  • Arabidopsis / genetics*
  • Base Sequence
  • Datasets as Topic
  • Gene Expression Profiling / methods*
  • Genes, Plant
  • High-Throughput Nucleotide Sequencing / methods*
  • Protein Isoforms / analysis*
  • RNA Splicing
  • RNA, Messenger / analysis*
  • Reference Values
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA / methods*
  • Software
  • Transcriptome


  • Protein Isoforms
  • RNA, Messenger