Author Identifier (ORCID)
Angéla Juhász: https://orcid.org/0000-0002-4317-2027
Utpal Bose: https://orcid.org/0000-0003-1156-6504
Michelle L. Colgrave: https://orcid.org/0000-0001-8463-805X
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.
Document Type
Journal Article
Date of Publication
12-1-2025
Volume
16
Issue
1
PubMed ID
41053037
Publication Title
Nature Communications
Publisher
Nature
School
Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science / School of Science
RAS ID
88263
Funders
Australian Research Council / Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR9816, BB/X011003/1, BB/M011216/1, BBS/E/ER/230003C, BBS/E/ER/230002B, BB/CCG1720/1) / Japan Society for the Promotion of Science (22H02316, 22H05179, 22K21352) / Coeliac Australia (G1005443) / Japan Science and Technology Agency (JPMJCR16O3)
Grant Number
ARC Number : CE200100012
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Comments
White, B., Lux, T., Rusholme-Pilcher, R., Juhász, A., Kaithakottil, G., Duncan, S., Simmonds, J., Rees, H., Wright, J., Colmer, J., Ward, S., Joynson, R., Coombes, B., Irish, N., Henderson, S., Barker, T., Chapman, H., Catchpole, L., Gharbi, K., . . . Koh, C. S. (2025). De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome. Nature Communications, 16. https://doi.org/10.1038/s41467-025-64046-1