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

Summary 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. Contents Summary 525 I. Introduction 525 II. Transcript‐specific expression quantification using a reference transcript dataset (RTD) 526 III. Why develop an RTD? 527 IV. How to create an RTD 527 V. RTDs for other plant species 529 VI.