BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification (2024)

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

BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. / Coulter, Max; Entizne, Juan Carlos; Guo, Wenbin et al.
In: Plant Journal, Vol. 111, No. 4, 08.2022, p. 1183-1202.

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

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

Coulter M, Entizne JC, Guo W, Bayer M, Wonneberger R, Milne L et al. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. Plant Journal. 2022 Aug;111(4):1183-1202. doi: 10.1111/tpj.15871

Coulter, Max ; Entizne, Juan Carlos ; Guo, Wenbin et al. / BaRTv2 : a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. In: Plant Journal. 2022 ; Vol. 111, No. 4. pp. 1183-1202.

@article{dbc8e213d3094fd08571857ef83dc40c,

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. 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,

doi = "10.1111/tpj.15871",

language = "English (US)",

volume = "111",

pages = "1183--1202",

journal = "Plant Journal",

issn = "0960-7412",

publisher = "Wiley-Blackwell",

number = "4",

}

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.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

Y1 - 2022/8

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

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U2 - 10.1111/tpj.15871

DO - 10.1111/tpj.15871

M3 - Article

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SN - 0960-7412

VL - 111

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EP - 1202

JO - Plant Journal

JF - Plant Journal

IS - 4

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