| Title: |
De Novo Annotation Reveals Transcriptomic Complexity Across the Hexaploid Wheat Pan-Genome |
| Authors: |
Rusholme-Pilcher, Rachel; White, Benjamen; Lux, Thomas; Juhasz, Angela; 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 J.; Bharti, Arvind K.; Colgrave, Michelle; Haerty, Wilfried; Uauy, Cristobal; Swarbreck, David; Borrill, Philippa; Poland, Jesse; Krattinger, Simon; Stein, Nils; Mayer, Klaus; Pozniak, Curtis; Spannagl, Manuel; Hall, Anthony; 10+ Wheat Genome Project |
| Publisher Information: |
Zenodo |
| Publication Year: |
2025 |
| Collection: |
Zenodo |
| Description: |
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. Analysis of these de novo annotations facilitated the identification of cultivar-specific genes and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars and cultivar-specific expression profiles. In a case study utilising both the newly constructed gene-based wheat pan-genome and pan-transcriptome, we demonstrate variation in the prolamin superfamily and immune-reactive proteins across cultivars.The datasets provided here are detailed in _README_additional_data.pdf |
| Document Type: |
text |
| Language: |
unknown |
| Relation: |
https://zenodo.org/records/16754571; oai:zenodo.org:16754571; https://doi.org/10.5281/zenodo.16754571 |
| DOI: |
10.5281/zenodo.16754571 |
| Availability: |
https://doi.org/10.5281/zenodo.16754571; https://zenodo.org/records/16754571 |
| Rights: |
Creative Commons Attribution 4.0 International ; cc-by-4.0 ; https://creativecommons.org/licenses/by/4.0/legalcode |
| Accession Number: |
edsbas.5206F64B |
| Database: |
BASE |