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

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. TheAtRTDwas formedbymerging transcripts fromTAIR10 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. TheAtRTD is a resource thatwill have immediate utility in analysingArabidopsis RNA-seqdata to quantify differential transcript abundance and expression.