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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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Nature Publishing Group
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/179274 |
| _version_ | 1855536361043394560 |
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| author | 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 |
| author_browse | Aquino, Catharine Ban, Tomohiro Bandi, Venkat Barker, Tom Bevan, Michael Bharti, Arvind Bin Xiao Fu Borrill, Philippa Bose, Utpal Brinton, Jemima Budak, Hikmet Byrns, Brook Catchpole, Leah Chalmers, Kenneth Chapman, Helen Chu Shin Koh Clark, Matthew Derek Clavijo, Bernardo Jose Cloutier, Sylvie Cockram, James Colgrave, Michelle Colmer, Joshua Coombes, Benedict Copetti, Dario Costamagna, Alejandro C. Deek, Jasline Delorean, Emily Distelfeld, Assaf Duncan, Susan Ens, Jennifer Fiebig, Anne Fobert, Pierre Fosker, Christine Fradgley, Nick Fritz, Allan Gao, Liangliang Garcia Accinelli, Gonzalo Gardner, Keith Gharbi, Karim Gundlach, Heidrun Gutierrez-Gonzalez, Juan J. Gutwin, Carl Haberer, Georg Haerty, Wilfried Hall, Anthony Halstead-Nussloch, Gwyneth Handa, Hirokazu Hatakeyama, Masaomi Heavens, Darren Henderson, Suzanne Himmelbach, Axel Hucl, Pierre J. Irish, Naomi Joynson, Ryan Juhász, Angéla Juliana, Philomin Kagale, Sateesh Kaithakottil, Gemy Kanamori, Hiroyuki Kassa, Mulualem T. Kawaura, Kanako Keeble-Gagnère, G. Keller, Beat Klymiuk, Valentyna Kobayashi, Fuminori Kolodziej, Markus C. Koo, Dal-Hoe Krasileva, Ksenia Krattinger, Simon Kuo, Tony Lang, Daniel Langridge, Peter Legg, Erik Lux, Thomas Mascher, Martin Mayer, Klaus McCartney, Curt McKenzie, Neil Melonek, Joanna Monat, Cécile Muehlbauer, Gary J. Murata, Kazuki Naamati, Guy Nabeka, Yusuke Nasuda, Shuhei Nilsen, Kirby T. Nunez Siri, Jorge N’Diaye, Amidou Okada, Moeko Paape, Timothy Padmarasu, Sudharsan Percival-Alwyn, Lawrence Poland, Jesse Pozniak, Curtis Ramirez Gonzalez, Ricardo Humberto Rees, Hannah Rusholme-Pilcher, Bachel Scholz, Uwe Sese, Jun Sharpe, Andrew G. Shimizu, Kentaro K. Shimizu-Inatsugi, Rie Simmonds, James Singh, Ravi Prakash Small, Ian Spannagl, Manuel Stein, Nils Steuernagel, Burkhard Swarbreck, David Tameshige, Toshiaki Tanaka, Tsuyoshi Thambugala, Dinushika Tibbets, Josquin Tsuji, Hiroyuki Uauy, Cristobal Venturini, Luca Walkowiak, Sean Ward, Sabrina White, Benjamen Wicker, Thomas Wiebe, Krystalee Wright, Jonathan Wu, Jianzhong |
| author_facet | 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 |
| author_sort | White, Benjamen |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| 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. 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. |
| format | Journal Article |
| id | CGSpace179274 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Nature Publishing Group |
| publisherStr | Nature Publishing Group |
| record_format | dspace |
| spelling | CGSpace1792742025-12-24T02:14:23Z De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome 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 wheat gene expression plant breeding transcriptomics 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. 2025-10 2025-12-23T22:35:08Z 2025-12-23T22:35:08Z Journal Article https://hdl.handle.net/10568/179274 en Open Access application/pdf Nature Publishing Group White, B., Lux, T., Rusholme-Pilcher, R., Juhász, A., Kaithakottil, G., Duncan, S., Simmonds, J., Rees, H., Wright, J., Colmer, J., Ward, S., Joynson, R., Coombes, B., Irish, N., Henderson, S., Barker, T., Chapman, H., Catchpole, L., Gharbi, K., . . . Koh, C. S. (2025). De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome. Nature Communications, 16(1), 8538. https://doi.org/10.1038/s41467-025-64046-1 |
| spellingShingle | wheat gene expression plant breeding transcriptomics 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 De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title | De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title_full | De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title_fullStr | De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title_full_unstemmed | De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title_short | De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome |
| title_sort | de novo annotation reveals transcriptomic complexity across the hexaploid wheat pan genome |
| topic | wheat gene expression plant breeding transcriptomics |
| url | https://hdl.handle.net/10568/179274 |
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denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT nabekayusuke denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT julianaphilomin denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT singhraviprakash denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT budakhikmet denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT smallian denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT melonekjoanna denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT cloutiersylvie denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT keeblegagnereg denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT tibbetsjosquin denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT langridgepeter denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT chalmerskenneth denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome AT distelfeldassaf denovoannotationrevealstranscriptomiccomplexityacrossthehexaploidwheatpangenome |