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Journal article
De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
Nature communications, Vol.16(1), 8538
2025
PMID: 41053037
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.
Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.
Details
- Title
- De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
- Authors/Creators
- Benjamen White - Norwich Research ParkThomas Lux - Helmholtz Zentrum MünchenRachel Rusholme-Pilcher - Norwich Research ParkAngéla Juhász - Australian Research CouncilGemy Kaithakottil - Norwich Research ParkSusan Duncan - Norwich Research ParkJames Simmonds - John Innes CentreHannah Rees - Earlham InstituteJonathan Wright - Earlham InstituteJoshua Colmer - Norwich Research ParkSabrina Ward - Norwich Research ParkRyan Joynson - Norwich Research ParkBenedict Coombes - Norwich Research ParkNaomi Irish - Norwich Research ParkSuzanne Henderson - Norwich Research ParkTom Barker - Norwich Research ParkHelen Chapman - Norwich Research ParkLeah Catchpole - Norwich Research ParkKarim Gharbi - Norwich Research ParkUtpal Bose - Australian Research CouncilMoeko Okada - Niigata UniversityHirokazu Handa - Kyoto Prefectural UniversityShuhei Nasuda - Kyoto UniversityKentaro K. Shimizu - University of ZurichHeidrun Gundlach - Helmholtz Zentrum MünchenDaniel Lang - Helmholtz Zentrum MünchenGuy Naamati - European Bioinformatics InstituteErik J. Legg - Syngenta (United States)Arvind K. Bharti - Syngenta (United States)Michelle L. Colgrave - Australian Research CouncilWilfried Haerty - Earlham InstituteCristobal Uauy - Norwich Research ParkDavid Swarbreck - Norwich Research ParkPhilippa Borrill - Norwich Research ParkJesse A. Poland - King Abdullah University of Science and TechnologySimon G. Krattinger - King Abdullah University of Science and TechnologyNils Stein - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Klaus F. X. Mayer - Plant (United States)Curtis Pozniak - University of SaskatchewanManuel Spannagl - Murdoch UniversityAnthony Hall - University of East Anglia10+ Wheat Genome Project
- Publication Details
- Nature communications, Vol.16(1), 8538
- Publisher
- Nature Publishing Group UK
- Grant note
- BB/M011216/1; BB/CCG1720/1; BBX011089/1; BB/X011003/1; BB/M011216/1 / RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) (https://doi.org/10.13039/501100000268)
- Identifiers
- 991005818348607891
- Copyright
- © The Author(s) 2025
- Murdoch Affiliation
- Centre for Crop and Food Innovation
- Language
- English
- Resource Type
- Journal article
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