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

Guo, Wenbin; Schreiber, Miriam; Marosi, Vanda B.; Bagnaresi, Paolo; Jorgensen, Morten Egevang; Braune, Katarzyna B.; Chalmers, Ken; Chapman, Brett; Dang, Viet; Dockter, Christoph; Fiebig, Anne; Fincher, Geoffrey B.; Fricano, Agostino; Fuller, John; Haaning, Allison; Haberer, Georg; Himmelbach, Axel; Jayakodi, Murukarthick; Jia, Yong; Kamal, Nadia; Langridge, Peter; Li, Chengdao; Lu, Qiongxian; Lux, Thomas; Mascher, Martin; Mayer, Klaus F. X.; Mccallum, Nicola; Milne, Linda; Muehlbauer, Gary J.; Nielsen, Martin T. S.; Padmarasu, Sudharsan; Pedas, Pai Rosager; Pillen, Klaus; Pozniak, Curtis; Rasmussen, Magnus W.; Sato, Kazuhiro; Schmutzer, Thomas; Scholz, Uwe; Schueler, Danuta; Simkova, Hana; Skadhauge, Birgitte; Stein, Nils; Thomsen, Nina W.; Voss, Cynthia; Wang, Penghao; Wonneberger, Ronja; Zhang, Xiao-Qi; Zhang, Guoping; Cattivelli, Luigi; Spannagl, Manuel; Bayer, Micha; Simpson, Craig; Zhang, Runxuan; Waugh, Robbie

doi:10.1038/s41588-024-02069-y

Research article2025Peer reviewedOpen access

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

Guo, Wenbin; Schreiber, Miriam; Marosi, Vanda B.; Bagnaresi, Paolo; Jorgensen, Morten Egevang; Braune, Katarzyna B.; Chalmers, Ken; Chapman, Brett; Dang, Viet; Dockter, Christoph; Fiebig, Anne; Fincher, Geoffrey B.; Fricano, Agostino; Fuller, John; Haaning, Allison; Haberer, Georg; Himmelbach, Axel; Jayakodi, Murukarthick; Jia, Yong; Kamal, Nadia;
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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.

Published in

Nature Genetics
2025, volume: 57, number: 2, pages: 441-450
Publisher: NATURE PORTFOLIO

SLU Authors

Wonneberger, Ronja
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
- The James Hutton Institute

UKÄ Subject classification

Genetics and Breeding in Agricultural Sciences

Publication identifier

DOI: https://doi.org/10.1038/s41588-024-02069-y

Permanent link to this page (URI)

https://res.slu.se/id/publ/140645