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

3 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

Fingerprint

RNA Sequence Analysis
alternative splicing
Alternative Splicing
sequence analysis
RNA
gene expression regulation
Gene Expression Regulation
Systems Analysis
Transcriptome
transcriptome
genes
transcription (genetics)
Gene Expression
Datasets
Genes

Keywords

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

Cite this

@article{21dd9db31d224423b940235227b717e5,
title = "High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants",
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.",
keywords = "alternative splicing, Arabidopsis reference transcript dataset (AtRTD2), gene expression, reference transcript dataset (RTD), RNA-sequencing, SALMON",
author = "Brown, {John W. S.} and Calixto, {Cristiane P. G.} and Runxuan Zhang",
note = "Biotechnology and Biological Sciences Research Council (BBSRC) Grant Number: BB/K006568/1, Scottish Government Rural and Environment Science and Analytical Services.",
year = "2017",
month = "1",
doi = "10.1111/nph.14208",
language = "English",
volume = "213",
pages = "525--530",
journal = "New Phytologist",
issn = "0028-646X",
publisher = "Wiley",
number = "2",

}

High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. / Brown, John W. S. (Lead / Corresponding author); Calixto, Cristiane P. G.; Zhang, Runxuan.

In: New Phytologist, Vol. 213, No. 2, 01.2017, p. 525-530.

Research output: Contribution to journalReview article

TY - JOUR

T1 - High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants

AU - Brown, John W. S.

AU - Calixto, Cristiane P. G.

AU - Zhang, Runxuan

N1 - Biotechnology and Biological Sciences Research Council (BBSRC) Grant Number: BB/K006568/1, Scottish Government Rural and Environment Science and Analytical Services.

PY - 2017/1

Y1 - 2017/1

N2 - 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.

AB - 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.

KW - alternative splicing

KW - Arabidopsis reference transcript dataset (AtRTD2)

KW - gene expression

KW - reference transcript dataset (RTD)

KW - RNA-sequencing

KW - SALMON

U2 - 10.1111/nph.14208

DO - 10.1111/nph.14208

M3 - Review article

VL - 213

SP - 525

EP - 530

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

IS - 2

ER -