Additional Data: De Novo Annotation Reveals Transcriptomic Complexity Across the Hexaploid Wheat Pan-Genome
Creators
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Rusholme-Pilcher, Rachel
(Project member)1
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White, Benjamen
(Project member)1
- Lux, Thomas (Project member)2
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Juhasz, Angela
(Project member)3
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Kaithakottil, Gemy
(Project member)1
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Duncan, Susan
(Project member)1
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Simmonds, James
(Project member)4
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Rees, Hannah
(Project member)1
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Wright, Jonathan
(Project member)1
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Colmer, Joshua
(Project member)1
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Ward, Sabrina
(Project member)1, 5
- Joynson, Ryan (Project member)1, 6
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Coombes, Benedict
(Project member)1
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Irish, Naomi
(Project member)1
- Henderson, Suzanne (Project member)1
- Barker, Tom (Project member)1
- Chapman, Helen (Project member)1
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Catchpole, Leah
(Project member)1
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Gharbi, Karim
(Project member)1
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Bose, Utpal
(Project member)7, 8
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Okada, Moeko
(Project member)9
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HANDA, Hirokazu
(Project member)10
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Nasuda, Shuhei
(Project member)11
- Shimizu, Kentaro K. (Project member)1
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Gundlach, Heidrun
(Project member)12
- Lang, Daniel (Project member)2
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Naamati, Guy
(Project member)13
- Legg, Erik J. (Project member)14
- Bharti, Arvind K. (Project member)14
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Colgrave, Michelle
(Project member)3
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Haerty, Wilfried
(Project member)1
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Uauy, Cristobal
(Project member)4
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Swarbreck, David
(Project member)1
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Borrill, Philippa
(Project member)4
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Poland, Jesse
(Project member)15
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Krattinger, Simon
(Project member)15
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Stein, Nils
(Project member)16, 17
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Mayer, Klaus
(Project member)2, 18
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Pozniak, Curtis
(Project member)19
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Spannagl, Manuel
(Project member)12
- Hall, Anthony (Project member)1
- 10+ Wheat Genome Project (Project member)
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1.
Earlham Institute
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2.
Helmholtz Munich
- 3. Edith Cowan University
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4.
John Innes Centre
- 5. The Earlham Institute
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6.
Limagrain (France)
- 7. Commonwealth Scientific and Industrial Research Organisation
- 8. CSIRO Queensland Bioscience Precinct
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9.
Niigata University
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10.
Kyoto Prefectural University
- 11. Kyoto University
- 12. Helmholtz Center Munich
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13.
European Molecular Biology Laboratory - European Bioinformatics Institute
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14.
Syngenta (United States)
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15.
King Abdullah University of Science and Technology
- 16. Georg-August-University
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17.
Leibniz Institute of Plant Genetics and Crop Plant Research
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18.
Technical University of Munich
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19.
University of Saskatchewan
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_contents.xlsx