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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 (2025)
Verlagsversion Forschungsdaten 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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Alignment; Rna; Highlights; Tandem; Hisat
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Zeitschrift Nature Communications
Quellenangaben Band: 16, Heft: 1, Seiten: , Artikelnummer: 8538 Supplement: ,
Verlag Nature Publishing Group
Verlagsort London
Begutachtungsstatus Peer reviewed
Institut(e) Research Unit Plant Genome and Systems Biology (PGSB)
Förderungen BMBF
BBSRC National Capability in Genomics and Single Cell Analysis
Earlham Institute Strategic Programme Grant Decoding Biodiversity
Norwich Research Park Biosciences Doctoral Training Partnership grant
Australian Research Council Centre of Excellence for Innovations in Peptide
MEXT JSPS KAKENHI
Swiss National Science Foundation
Japan Science and Technology Agency
UZH Global Strategy and Partnerships Funding Scheme of the University of Zurich
RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)