De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome

Benjamen White, Thomas Lux, Rachel Rusholme-Pilcher, Angéla Juhász, Gemy Kaithakottil, Susan Duncan, James Simmonds, Hannah Rees, Jonathan Wright, Joshua Colmer, Sabrina Ward, Ryan Joynson, Benedict Coombes, Naomi Irish, Suzanne Henderson, Tom Barker, Helen Chapman, Leah Catchpole, Karim Gharbi, Utpal Bose, Moeko Okada, Hirokazu Handa, Shuhei Nasuda, Kentaro K. Shimizu, Heidrun Gundlach, Daniel Lang, Guy Naamati, Erik J. Legg, Arvind K. Bharti, Michelle L. Colgrave, Wilfried Haerty, Cristobal Uauy, David Swarbreck, Philippa Borrill, Jesse A. Poland, Simon G. Krattinger, Nils Stein, Klaus F. X. Mayer, Curtis Pozniak, Manuel Spannagl () and Anthony Hall ()
Additional contact information
Benjamen White: Norwich Research Park
Thomas Lux: German Research Center for Environmental Health
Rachel Rusholme-Pilcher: Norwich Research Park
Angéla Juhász: Edith Cowan University
Gemy Kaithakottil: Norwich Research Park
Susan Duncan: Norwich Research Park
James Simmonds: Norwich Research Park
Hannah Rees: Norwich Research Park
Jonathan Wright: Norwich Research Park
Joshua Colmer: Norwich Research Park
Sabrina Ward: Norwich Research Park
Ryan Joynson: Norwich Research Park
Benedict Coombes: Norwich Research Park
Naomi Irish: Norwich Research Park
Suzanne Henderson: Norwich Research Park
Tom Barker: Norwich Research Park
Helen Chapman: Norwich Research Park
Leah Catchpole: Norwich Research Park
Karim Gharbi: Norwich Research Park
Utpal Bose: Edith Cowan University
Moeko Okada: University of Zurich
Hirokazu Handa: Kyoto Prefectural University
Shuhei Nasuda: Kyoto University
Kentaro K. Shimizu: University of Zurich
Heidrun Gundlach: German Research Center for Environmental Health
Daniel Lang: German Research Center for Environmental Health
Guy Naamati: EMBL-EBI, Wellcome Genome Campus
Erik J. Legg: Research Triangle Park
Arvind K. Bharti: Research Triangle Park
Michelle L. Colgrave: Edith Cowan University
Wilfried Haerty: Norwich Research Park
Cristobal Uauy: Norwich Research Park
David Swarbreck: Norwich Research Park
Philippa Borrill: Norwich Research Park
Jesse A. Poland: King Abdullah University of Science and Technology (KAUST)
Simon G. Krattinger: King Abdullah University of Science and Technology (KAUST)
Nils Stein: Martin Luther University of Halle-Wittenberg
Klaus F. X. Mayer: German Research Center for Environmental Health
Curtis Pozniak: The University of Saskatchewan
Manuel Spannagl: German Research Center for Environmental Health
Anthony Hall: Norwich Research Park

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Wheat is the most widely cultivated crop in the world, with over 215 million hectares grown annually. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome-level the genomes of nine wheat cultivars, uncovering genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars across multiple tissues. Using the de novo annotations we identify cultivar-specific genes and define the core and dispensable genomes. Expression analysis across cultivars and tissues reveals conservation in expression between a large core set of homeologous genes, in addition to widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. We utilise both the newly constructed gene-based wheat pan-genome and pan-transcriptome, demonstrating variation in the prolamin superfamily and immune-reactive proteins across cultivars.

Date: 2025
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DOI: 10.1038/s41467-025-64046-1

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