De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
Benjamen White, Thomas Lux, Rachel Rusholme‐Pilcher, Angéla Juhász, Gemy Kaithakottil, Susan Duncan, James Simmonds, Hannah Rees, Jonathan Wright, Joshua Colmer, Ben J. Ward, Ryan Joynson, Benedict Coombes, Naomi Irish, S. M. Henderson, Tom Barker, Helen Chapman, Leah Catchpole, Karim Gharbi, Utpal Bose, Moeko Okada, Hirokazu Handa, Shuhei Nasuda, Kentaro K. Shimizu, Heidrun Gundlach, Daniel Lang, Guy Naamati, Erik Legg, Arvind K. Bharti, Michelle L. Colgrave, Wilfried Haerty, Cristóbal Uauy, David Swarbreck, Philippa Borrill, Jesse Poland, Simon G. Krattinger, Nils Stein, Klaus Mayer, Curtis Pozniak, 10+ Wheat Genome Project, Sean Walkowiak, Valentyna Klymiuk, Brook Byrns, Kirby T. Nilsen, Jennifer Ens, Krystalee Wiebe, Amidou N’Diaye, Pierre Hucl, Curtis Pozniak, Bin Xiao Fu, Liangliang Gao, Emily Delorean, Dal-Hoe Koo, Allen K. Fritz, Jesse Poland, Cécile Monat, Axel Himmelbach, Anne Fiebig, Sudharsan Padmarasu, Uwe Scholz, Martin Mascher, Georg Haberer, Mulualem T. Kassa, Pierre R. Fobert, Sateesh Kagale, Jemima Brinton, Ricardo H. Ramírez-González, Michael Bevan, Neil McKenzie, Burkhard Steuernagel, Markus C. Kolodziej, Simon G. Krattinger, Beat Keller, Thomas Wicker, Dinushika Thambugala, Curt A. McCartney, Venkat Bandi, Jorge Núñez Siri, Carl Gutwin, Catharine Aquino, Masaomi Hatakeyama, Dario Copetti, Gwyneth Halstead-Nussloch, Timothy Paape, Rie Shimizu‐Inatsugi, Kentaro K. Shimizu, Tomohiro Ban, Kanako Kawaura, Toshiaki Tameshige, Hiroyuki Tsuji, Luca Venturini, Matthew D. Clark, Bernardo Clavijo, Nigel Fosker, Gonzalo Garcia Accinelli, Darren Heavens, Ksenia V. Krasileva, Keith A. Gardner, Nick Fradgley, Lawrence Percival‐Alwyn
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.