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

• Published in: The New phytologist Vol. 208; no. 1; pp. 96 - 101
• Main Authors: Zhang, Runxuan, Calixto, Cristiane P. G., Tzioutziou, Nikoleta A., James, Allan B., Simpson, Craig G., Guo, Wenbin, Marquez, Yamile, Kalyna, Maria, Patro, Rob, Eyras, Eduardo, Barta, Andrea, Nimmo, Hugh G., Brown, John W. S.
• Format: Journal Article
• Language: English
• Published: England New Phytologist Trust 01-10-2015; Wiley Subscription Services, Inc; Wiley; John Wiley and Sons Inc
• Subjects: Abundance; Algorithms; Alternative Splicing; Arabidopsis; Arabidopsis - genetics; Arabidopsis thaliana; Base Sequence; Datasets; Datasets as Topic; DNA; Freshwater fishes; Gene expression; Gene Expression Profiling - methods; Gene sequencing; Genes; Genes, Plant; High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq); high resolution reverse transcription (HR RT)‐PCR; High-Throughput Nucleotide Sequencing - methods; Introns; Isoforms; Nucleic acids; Nucleotide sequence; PCR; Polymerase chain reaction; Protein isoforms; Protein Isoforms - analysis; Quantification; Rapid Report; Rapid reports; Ratios; Reference Values; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; Reverse transcription; Ribonucleic acid; RNA; RNA Splicing; RNA, Messenger - analysis; RNA‐sequencing (RNA‐seq); SAILFISH; SALMON; Sequence Analysis, RNA - methods; Software; Splicing; Transcription; Transcriptome; Transcripts per million; Arabidopsis thaliana; alternative splicing; Sailfish; Salmon; transcripts per million; RNA-sequencing (RNA-seq); high resolution reverse transcription (HR RT)-PCR
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.13545

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.