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White, B.* ; Lux, T. ; Rusholme-Pilcher, R.* ; Juhász, A.* ; Kaithakottil, G.* ; Duncan, S.R.* ; 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.* ; Bose, U.* ; Okada, M.* ; Handa, H.* ; Nasuda, S.* ; Shimizu, K.K.* ; Gundlach, H. ; Lang, D. ; Naamati, G.* ; Legg, E.J.* ; Bharti, A.K.* ; Colgrave, M.L.* ; Haerty, W.* ; Uauy, C.* ; Swarbreck, D.* ; Poland, J.A.* ; Krattinger, S.G.* ; Stein, N.* ; Mayer, K.F.X. ; Pozniak, C.* ; Spannagl, M. ; Hall, A.*

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

Nat. Commun. 16, 8538:8538 (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Journal Nature Communications
Quellenangaben Volume: 16, Issue: 1, Pages: 8538 Article Number: 8538 Supplement: ,
Publisher Nature Publishing Group
Publishing Place London
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)