High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants

John W. S. Brown (Lead / Corresponding author), Cristiane P. G. Calixto, Runxuan Zhang

Research output: Contribution to journalReview article

6 Citations (Scopus)

Abstract

Re-programming of the transcriptome involves both transcription and alternative splicing (AS). Some genes are regulated only at the AS level with no change in expression at the gene level. AS data must be incorporated as an essential aspect of the regulation of gene expression. RNA-sequencing (RNA-seq) can deliver both transcriptional and AS information, but accurate methods to analyse the added complexity in RNA-seq data are needed. The construction of a comprehensive reference transcript dataset (RTD) for a specific plant species, variety or accession, from all available sequence data, will immediately allow more robust analysis of RNA-seq data. RTDs will continually evolve and improve, a process that will be more efficient if resources across a community are shared and pooled.

Original languageEnglish
Pages (from-to)525-530
Number of pages6
JournalNew Phytologist
Volume213
Issue number2
Early online date23 Sep 2016
DOIs
Publication statusPublished - Jan 2017

Keywords

  • alternative splicing
  • Arabidopsis reference transcript dataset (AtRTD2)
  • gene expression
  • reference transcript dataset (RTD)
  • RNA-sequencing
  • SALMON

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