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

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. Her...

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Main Authors: White, Benjamen, Lux, Thomas, Rusholme-Pilcher, Bachel, Juhász, Angéla, Kaithakottil, Gemy, Duncan, Susan, Simmonds, James, Rees, Hannah, Wright, Jonathan, Colmer, Joshua, Ward, Sabrina, Joynson, Ryan, Coombes, Benedict, Irish, Naomi, Henderson, Suzanne, Barker, Tom, Chapman, Helen, Catchpole, Leah, Gharbi, Karim, Bose, Utpal, Okada, Moeko, Handa, Hirokazu, Nasuda, Shuhei, Shimizu, Kentaro K., Gundlach, Heidrun, Lang, Daniel, Naamati, Guy, Legg, Erik, Bharti, Arvind, Colgrave, Michelle, Haerty, Wilfried, Uauy, Cristobal, Swarbreck, David, Borrill, Philippa, Poland, Jesse, Krattinger, Simon, Stein, Nils, Mayer, Klaus, Pozniak, Curtis, Walkowiak, Sean, Klymiuk, Valentyna, Byrns, Brook, Nilsen, Kirby T., Ens, Jennifer, Wiebe, Krystalee, N’Diaye, Amidou, Hucl, Pierre J., Bin Xiao Fu, Gao, Liangliang, Delorean, Emily, Koo, Dal-Hoe, Fritz, Allan, Monat, Cécile, Himmelbach, Axel, Fiebig, Anne, Padmarasu, Sudharsan, Scholz, Uwe, Mascher, Martin, Haberer, Georg, Spannagl, Manuel, Kassa, Mulualem T., Fobert, Pierre, Kagale, Sateesh, Brinton, Jemima, Ramirez Gonzalez, Ricardo Humberto, Bevan, Michael, McKenzie, Neil, Steuernagel, Burkhard, Kolodziej, Markus C., Keller, Beat, Wicker, Thomas, Thambugala, Dinushika, McCartney, Curt, Bandi, Venkat, Nunez Siri, Jorge, Gutwin, Carl, Aquino, Catharine, Hatakeyama, Masaomi, Copetti, Dario, Halstead-Nussloch, Gwyneth, Paape, Timothy, Shimizu-Inatsugi, Rie, Ban, Tomohiro, Kawaura, Kanako, Tameshige, Toshiaki, Tsuji, Hiroyuki, Venturini, Luca, Clark, Matthew Derek, Clavijo, Bernardo Jose, Fosker, Christine, Garcia Accinelli, Gonzalo, Heavens, Darren, Krasileva, Ksenia, Hall, Anthony, Gardner, Keith, Fradgley, Nick, Percival-Alwyn, Lawrence, Cockram, James, Gutierrez-Gonzalez, Juan J., Muehlbauer, Gary J., Chu Shin Koh, Sharpe, Andrew G., Deek, Jasline, Costamagna, Alejandro C., Kanamori, Hiroyuki, Kobayashi, Fuminori, Tanaka, Tsuyoshi, Wu, Jianzhong, Kuo, Tony, Sese, Jun, Murata, Kazuki, Nabeka, Yusuke, Juliana, Philomin, Singh, Ravi Prakash, Budak, Hikmet, Small, Ian, Melonek, Joanna, Cloutier, Sylvie, Keeble-Gagnère, G., Tibbets, Josquin, Langridge, Peter, Chalmers, Kenneth, Distelfeld, Assaf
Format: Journal Article
Language:Inglés
Published: Nature Publishing Group 2025
Subjects:
wheat
gene expression
plant breeding
transcriptomics
Online Access:https://hdl.handle.net/10568/179274
Summary: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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