A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Runxuan Zhang, Cristiane P. G. Calixto, Yamile Marquez, Peter Venhuizen, Nikoleta A. Tzioutziou, Wenbin Guo, Mark Spensley, Juan Carlos Entizne, Dominika Lewandowska, Sara ten Have, Nicolas Frei dit Frey, Heribert Hirt, Allan B. James, Hugh G. Nimmo, Andrea Barta, Maria Kalyna, John W. S. Brown (Lead / Corresponding author)

Research output: Contribution to journalArticle

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Abstract

Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34,212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
Original languageEnglish
Pages (from-to)5061-5073
Number of pages13
JournalNucleic Acids Research
Volume45
Issue number9
Early online date11 Apr 2017
DOIs
Publication statusPublished - 19 May 2017

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Alternative Splicing
Transcriptome
Arabidopsis
Protein Isoforms
RNA
RNA Sequence Analysis
Gene Expression Regulation
Genes
Genome

Keywords

  • RNA-seq
  • Alternative splicing
  • Arabidopsis thaliana
  • Transcript quantification
  • Transcript assembly

Cite this

Zhang, Runxuan ; Calixto, Cristiane P. G. ; Marquez, Yamile ; Venhuizen, Peter ; Tzioutziou, Nikoleta A. ; Guo, Wenbin ; Spensley, Mark ; Entizne, Juan Carlos ; Lewandowska, Dominika ; ten Have, Sara ; Frei dit Frey, Nicolas ; Hirt, Heribert ; James, Allan B. ; Nimmo, Hugh G. ; Barta, Andrea ; Kalyna, Maria ; Brown, John W. S. / A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. In: Nucleic Acids Research. 2017 ; Vol. 45, No. 9. pp. 5061-5073.
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abstract = "Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34,212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.",
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Zhang, R, Calixto, CPG, Marquez, Y, Venhuizen, P, Tzioutziou, NA, Guo, W, Spensley, M, Entizne, JC, Lewandowska, D, ten Have, S, Frei dit Frey, N, Hirt, H, James, AB, Nimmo, HG, Barta, A, Kalyna, M & Brown, JWS 2017, 'A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing', Nucleic Acids Research, vol. 45, no. 9, pp. 5061-5073. https://doi.org/10.1093/nar/gkx267

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. / Zhang, Runxuan; Calixto, Cristiane P. G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten Have, Sara; Frei dit Frey, Nicolas; Hirt, Heribert ; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria; Brown, John W. S. (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 45, No. 9, 19.05.2017, p. 5061-5073.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

AU - Zhang, Runxuan

AU - Calixto, Cristiane P. G.

AU - Marquez, Yamile

AU - Venhuizen, Peter

AU - Tzioutziou, Nikoleta A.

AU - Guo, Wenbin

AU - Spensley, Mark

AU - Entizne, Juan Carlos

AU - Lewandowska, Dominika

AU - ten Have, Sara

AU - Frei dit Frey, Nicolas

AU - Hirt, Heribert

AU - James, Allan B.

AU - Nimmo, Hugh G.

AU - Barta, Andrea

AU - Kalyna, Maria

AU - Brown, John W. S.

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PY - 2017/5/19

Y1 - 2017/5/19

N2 - Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34,212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

AB - Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34,212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

KW - RNA-seq

KW - Alternative splicing

KW - Arabidopsis thaliana

KW - Transcript quantification

KW - Transcript assembly

U2 - 10.1093/nar/gkx267

DO - 10.1093/nar/gkx267

M3 - Article

VL - 45

SP - 5061

EP - 5073

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 9

ER -