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

TY - JOUR

T1 - AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript - specific expression in Arabidopsis thaliana

AU - Zhang, Runxuan

AU - Calixto, Cristiane P. G.

AU - Tzioutziou, Nikoleta A.

AU - James, Allan B.

AU - Simpson, Craig G.

AU - Guo, Wenbin

AU - Marquez, Yamile

AU - Kalyna, Maria

AU - Patro, Rob

AU - Eyras, Eduardo

AU - Barta, Andrea

AU - Nimmo, Hugh G.

AU - Brown, John W. S.

N1 - © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

PY - 2015/10

Y1 - 2015/10

N2 - 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.

AB - 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.

KW - Arabidopsis thaliana

KW - Alternative splicing

KW - High resolution reverse transcription (HR RT)-PCR

KW - RNA-sequencing (RNA-seq)

KW - Sailfish

KW - Salmon

KW - Transcripts per million

UR - https://www.scopus.com/pages/publications/84940467101

U2 - 10.1111/nph.13545

DO - 10.1111/nph.13545

M3 - Article

C2 - 26111100

SN - 0028-646X

VL - 208

SP - 96

EP - 101

JO - New Phytologist

JF - New Phytologist

IS - 1

ER -