BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Max Coulter; Juan Carlos Entizne; Wenbin Guo; Micha Bayer; Ronja Wonneberger; Linda Milne; Miriam Schreiber; Allison Haaning; Gary J. Muehlbauer; Nicola McCallum; John Fuller; Craig Simpson; Nils Stein; John W. S. Brown; Robbie Waugh; Runxuan Zhang

doi:10.1111/tpj.15871

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Max Coulter, Juan Carlos Entizne, Wenbin Guo, Micha Bayer, Ronja Wonneberger, Linda Milne, Miriam Schreiber, Allison Haaning, Gary J. Muehlbauer, Nicola McCallum, John Fuller, Craig Simpson, Nils Stein, John W. S. Brown, Robbie Waugh, Runxuan Zhang (Lead / Corresponding author)

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21 Citations (Scopus)

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Abstract

Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

Original language	English
Pages (from-to)	1183-1202
Number of pages	20
Journal	Plant Journal
Volume	111
Issue number	4
Early online date	15 Jun 2022
DOIs	https://doi.org/10.1111/tpj.15871
Publication status	Published - 16 Aug 2022

Keywords

Iso-seq
RNA-seq
barley
reference transcript datasets
transcriptomic analysis

ASJC Scopus subject areas

Genetics
Plant Science
Cell Biology

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10.1111/tpj.15871Licence: CC BY

Final published versionFinal published version, 2.72 MBLicence: CC BY

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Coulter, M., Entizne, J. C., Guo, W., Bayer, M., Wonneberger, R., Milne, L., Schreiber, M., Haaning, A., Muehlbauer, G. J., McCallum, N., Fuller, J., Simpson, C., Stein, N., Brown, J. W. S., Waugh, R., & Zhang, R. (2022). BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. Plant Journal, 111(4), 1183-1202. https://doi.org/10.1111/tpj.15871

@article{2e7d4c26522d4c93a3b133ae1344a50d,

title = "BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification",

abstract = "Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.",

keywords = "Iso-seq, RNA-seq, barley, reference transcript datasets, transcriptomic analysis",

author = "Max Coulter and Entizne, {Juan Carlos} and Wenbin Guo and Micha Bayer and Ronja Wonneberger and Linda Milne and Miriam Schreiber and Allison Haaning and Muehlbauer, {Gary J.} and Nicola McCallum and John Fuller and Craig Simpson and Nils Stein and Brown, {John W. S.} and Robbie Waugh and Runxuan Zhang",

note = "Funding Information: The authors acknowledge the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the {"}UK's Crop Diversity Bioinformatics HPC{"} (BBSRC grant BB/S019669/1), use of which has contributed to the results reported. We thank Susanne K{\"o}nig and Axel Himmelbach from IPK Gatersleben for preparing and sequencing the Iso‐seq libraries. The authors acknowledge the support of the Biotechnology and Biological Sciences Research Council (Grant Numbers BB/S020160/1, BB/S004610/1, BB/R014582/1) to MC, RZ, MB, WG, RWa and JWSB; The Rural & Environment Science & Analytical Services Division of the Scottish Government (Grant Number SRP WP2.1 and 2.2) to RZ, WG, MB, LM, NM, MS, CS, JF and RWa; a joint PhD scholarship from the James Hutton Institute and the University of Dundee/BBSRC DTP (BB/M010996/1) to JSWB, RZ and JCE; German Research Council (DFG) (Grant number STE 1102/15‐1) to NS and RWo; and the National Science Foundation (Grant number ERA‐CAPS 1844331) to GM and AH. Publisher Copyright: {\textcopyright} 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.",

year = "2022",

month = aug,

day = "16",

doi = "10.1111/tpj.15871",

language = "English",

volume = "111",

pages = "1183--1202",

journal = "Plant Journal",

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Coulter, M, Entizne, JC, Guo, W, Bayer, M, Wonneberger, R, Milne, L, Schreiber, M, Haaning, A, Muehlbauer, GJ, McCallum, N, Fuller, J, Simpson, C, Stein, N, Brown, JWS , Waugh, R & Zhang, R 2022, 'BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification', Plant Journal, vol. 111, no. 4, pp. 1183-1202. https://doi.org/10.1111/tpj.15871

TY - JOUR

T1 - BaRTv2

T2 - A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

AU - Coulter, Max

AU - Entizne, Juan Carlos

AU - Guo, Wenbin

AU - Bayer, Micha

AU - Wonneberger, Ronja

AU - Milne, Linda

AU - Schreiber, Miriam

AU - Haaning, Allison

AU - Muehlbauer, Gary J.

AU - McCallum, Nicola

AU - Fuller, John

AU - Simpson, Craig

AU - Stein, Nils

AU - Brown, John W. S.

AU - Waugh, Robbie

AU - Zhang, Runxuan

N1 - Funding Information: The authors acknowledge the Research/Scientific Computing teams at The James Hutton Institute and NIAB for providing computational resources and technical support for the "UK's Crop Diversity Bioinformatics HPC" (BBSRC grant BB/S019669/1), use of which has contributed to the results reported. We thank Susanne König and Axel Himmelbach from IPK Gatersleben for preparing and sequencing the Iso‐seq libraries. The authors acknowledge the support of the Biotechnology and Biological Sciences Research Council (Grant Numbers BB/S020160/1, BB/S004610/1, BB/R014582/1) to MC, RZ, MB, WG, RWa and JWSB; The Rural & Environment Science & Analytical Services Division of the Scottish Government (Grant Number SRP WP2.1 and 2.2) to RZ, WG, MB, LM, NM, MS, CS, JF and RWa; a joint PhD scholarship from the James Hutton Institute and the University of Dundee/BBSRC DTP (BB/M010996/1) to JSWB, RZ and JCE; German Research Council (DFG) (Grant number STE 1102/15‐1) to NS and RWo; and the National Science Foundation (Grant number ERA‐CAPS 1844331) to GM and AH. Publisher Copyright: © 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

PY - 2022/8/16

Y1 - 2022/8/16

N2 - Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

AB - Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

KW - Iso-seq

KW - RNA-seq

KW - barley

KW - reference transcript datasets

KW - transcriptomic analysis

UR - http://www.scopus.com/inward/record.url?scp=85134153432&partnerID=8YFLogxK

U2 - 10.1111/tpj.15871

DO - 10.1111/tpj.15871

M3 - Article

C2 - 35704392

SN - 0960-7412

VL - 111

SP - 1183

EP - 1202

JO - Plant Journal

JF - Plant Journal

IS - 4

ER -

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

A Reference Transcript Database for Improved Analysis of RNA-seq Data from Barley

16 ERA-CAPS Barley Yield Associated Networks (Joint with IPK Gatersleben as lead and University of Minnesota)

Automated generation of high quality transcriptome annotations and their coding characterisation

Cite this

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

A Reference Transcript Database for Improved Analysis of RNA-seq Data from Barley

16 ERA-CAPS Barley Yield Associated Networks (Joint with IPK Gatersleben as lead and University of Minnesota)

Student theses

Automated generation of high quality transcriptome annotations and their coding characterisation

Cite this