A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.

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Publication Details

Journal
Nature Genetics
Published
2025-02-01
DOI
https://doi.org/10.1038/s41588-024-02069-y
Citations
34
Primary Topic
Wheat and Barley Genetics and Pathology
Type
article
Field-Weighted Citation Impact
59.49

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article

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

Peter Langridge, Curtis Jerry Pozniak, Klaus Pillen, Murukarthick Jayakodi et al.
34 citations
Nature Genetics
Wheat and Barley Genetics and Pathology
59.49
article

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

Peter Langridge, Curtis Jerry Pozniak, Klaus Pillen, Murukarthick Jayakodi, Nicola McCallum, Geoffrey B. Fincher, Cynthia Voss, Thomas Schmutzer, K. J. Chalmers, Martin Toft Simmelsgaard Nielsen, Ronja Wonneberger, Danuta Schüler, Agostino Fricano, Brett Chapman, Miriam Schreiber, Martin Mascher, Thomas Lux, Vanda Marosi, Gary J. Muehlbauer, Viet Dang, Micha Bayer, John Fuller, Craig G. Simpson, Qiongxian Lu, Birgitte Skadhauge, Klaus Mayer, Paolo Bagnaresi, Nils Stein, Yong Jia, Christoph Dockter, Allison Haaning, Uwe Scholz, Georg Haberer, Anne Fiebig, Chengdao Li, Nadia Kamal, Pai Pedas, Linda Milne, Luigi Cattivelli, Sudharsan Padmarasu, Robbie Waugh, Kazuhiro Sato, Magnus Wohlfahrt Rasmussen, Runxuan Zhang, Axel Himmelbach, Wenbin Guo, M. Spannagl, Morten Egevang Jørgensen, Penghao Wang, Katarzyna Braune, Guoping Zhang, Xiaoqi Zhang, Hana Šimková, Nina W. Thomsen
article en
34 citations

Abstract

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.

Nature GeneticsVol. 57(2)
Roskilde University (DK), University of Minnesota (US), James Hutton Institute (GB), Okayama University (JP), Texas A&M University System (US), Murdoch University (AU), University of Dundee (GB), Yangtze University (CN), Carlsberg Laboratory (DK), Wine Australia (AU), Swedish University of Agricultural Sciences (SE), Helmholtz Zentrum München (DE), Lishui University (CN), University of Saskatchewan (CA), Department of Primary Industries and Regional Development (AU), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), Research Centre for Olive Growing and Olive Oil Industry (IT), Kazusa DNA Research Institute (JP), Czech Academy of Sciences, Institute of Experimental Botany (CZ), The University of Adelaide (AU), Technical University of Munich (DE), Martin Luther University Halle-Wittenberg (DE), Zhejiang University (CN), Texas A&M University (US)
Biotechnology and Biological Sciences Research Council
Life in Land
Openalex Percentile: Top 0%
Wheat and Barley Genetics and Pathology
59.49
DOIOpen Access PDFOpenAlex
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