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

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

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 (US)
Pages (from-to)	1183-1202
Number of pages	20
Journal	Plant Journal
Volume	111
Issue number	4
DOIs	https://doi.org/10.1111/tpj.15871
State	Published - Aug 2022

Bibliographical 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 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.

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.

Keywords

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

PubMed: MeSH publication types

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

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10.1111/tpj.15871

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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

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

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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.",

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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",

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year = "2022",

month = aug,

doi = "10.1111/tpj.15871",

language = "English (US)",

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AU - Guo, Wenbin

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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.

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AU - Zhang, Runxuan

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

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

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