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

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DOI

Resolve DOI: https://doi.org/10.1038/s41467-025-64046-1

Author

Search for: White, Benjamen ORCID identifier: https://orcid.org/0000-0003-4391-3945; Search for: Lux, Thomas ORCID identifier: https://orcid.org/0000-0002-5543-1911; Search for: Rusholme-Pilcher, Rachel ORCID identifier: https://orcid.org/0000-0003-0000-0038; Search for: Juhász, Angéla ORCID identifier: https://orcid.org/0000-0002-4317-2027; Search for: Kaithakottil, Gemy ORCID identifier: https://orcid.org/0000-0003-1360-7808; Search for: Duncan, Susan ORCID identifier: https://orcid.org/0000-0001-9581-1145; Search for: Simmonds, James ORCID identifier: https://orcid.org/0000-0003-4936-1694; Search for: Rees, Hannah; Search for: Wright, Jonathan ORCID identifier: https://orcid.org/0000-0001-6471-8749; Search for: Colmer, Joshua; Search for: Ward, Sabrina; Search for: Joynson, Ryan; Search for: Coombes, Benedict ORCID identifier: https://orcid.org/0000-0003-4956-1055; Search for: Irish, Naomi; Search for: Henderson, Suzanne; Search for: Barker, Tom; Search for: Chapman, Helen; Search for: Catchpole, Leah; Search for: Gharbi, Karim ORCID identifier: https://orcid.org/0000-0003-1092-4488; Search for: Bose, Utpal; Search for: Okada, Moeko ORCID identifier: https://orcid.org/0000-0002-4398-5917; Search for: Handa, Hirokazu; Search for: Nasuda, Shuhei; Search for: Shimizu, Kentaro K.; Search for: Gundlach, Heidrun ORCID identifier: https://orcid.org/0000-0002-6757-0943; Search for: Lang, Daniel ORCID identifier: https://orcid.org/0000-0002-2166-0716; Search for: Naamati, Guy; Search for: Legg, Erik J.; Search for: Bharti, Arvind K.; Search for: Colgrave, Michelle L.ORCID identifier: https://orcid.org/0000-0001-8463-805X; Search for: Haerty, Wilfried ORCID identifier: https://orcid.org/0000-0003-0111-191X; Search for: Uauy, Cristobal ORCID identifier: https://orcid.org/0000-0002-9814-1770; Search for: Swarbreck, David ORCID identifier: https://orcid.org/0000-0002-5453-1013; Search for: Borrill, Philippa ORCID identifier: https://orcid.org/0000-0002-7623-8256; Search for: Poland, Jesse A.ORCID identifier: https://orcid.org/0000-0002-7856-1399; Search for: Krattinger, Simon G.; Search for: Stein, Nils ORCID identifier: https://orcid.org/0000-0003-3011-8731; Search for: Mayer, Klaus F. 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Affiliation

National Research Council Canada. Aquatic and Crop Resource Development

Format

Text, Article

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 published

2025-10-06

Publisher

Springer Nature

Licence

Creative Commons, Attribution 4.0 International (CC BY 4.0)
https://creativecommons.org/licenses/by/4.0/

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Language

English

Peer reviewed

Yes

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Record identifier

d7833908-cc57-4d2b-b258-d1b3d365fb36

Record created

2026-05-15

Record modified

2026-06-25

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National Research Council Canada

Date modified:: 2026-07-12