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
- Sabrina Ward
- Ryan Joynson
- Benedict Coombes
- Naomi Irish
- Suzanne 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 J. Legg
- Arvind K. Bharti
- Michelle L. Colgrave
- Wilfried Haerty
- Cristobal Uauy
- David Swarbreck
- Philippa Borrill
- Jesse A. Poland
- Simon G. Krattinger
- Nils Stein
- Klaus F. X. Mayer
- Curtis Pozniak
- Sean Walkowiak
- Valentyna Klymiuk
- Brook Byrns
- Kirby Nilsen
- Jennifer Ens
- Krystalee Wiebe
- Amidou N’Diaye
- Pierre J. Hucl
- Curtis J. Pozniak
- Bin Xiao Fu
- Liangliang Gao
2025-10-06
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.