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.

Carlsberg Research Laboratory Copenhagen Denmark

Chair of Crop Plant Genetics Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Germany

Chair of Plant Breeding Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Germany

College of Agriculture and Biotechnology Zhejiang University Hangzhou China

College of Agriculture Yangtze University Jinzhou China

Council for Agriculture Research and Economics Research Centre for Genomics and Bioinformatics Fiorenzuola d'Arda Italy

CREA Research Centre for Olive Fruit and Citrus Crops Forlì Italy

Department of Agronomy and Plant Genetics University of Minnesota St Paul MN USA

Department of Molecular Life Sciences Computational Plant Biology School of Life Sciences Technical University of Munich Freising Germany

Department of Plant Breeding Swedish University of Agricultural Sciences Uppsala Sweden

Department of Plant Sciences and Crop Development Centre University of Saskatchewan Saskatoon Saskatchewan Canada

Department of Primary Industry and Regional Development Western Australia South Perth Western Australia Australia

Department of Soil and Crop Sciences Texas A and M University College Station TX USA

DLF Roskilde Denmark

Higentec Breeding Innovation Co Ltd Lishui China

Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

Institute of Plant Science and Resources Okayama University Kurashiki Japan

International Barley Hub Dundee Scotland

Kazusa DNA Research Institute Kisarazu Japan

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Seeland Germany

Minnesota Supercomputing Institute University of Minnesota Minneapolis MN USA

Plant Genome and Systems Biology Helmholtz Center Munich German Research Center for Environmental Health Neuherberg Germany

School of Agriculture Food and Wine University of Adelaide Waite Campus Urrbrae South Australia Australia

School of Life Sciences Technical University of Munich Freising Germany

School of Life Sciences University of Dundee Dundee UK

Texas A and M AgriLife Research Center at Dallas Texas A and M University System Dallas TX USA

Western Crop Genetics Alliance Food Futures Institute School of Agriculture Murdoch University Murdoch Western Australia Australia

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