Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome
Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/119697 |
| _version_ | 1855519103310102528 |
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| author | Bayer, Philipp E. Petereit, Jakob Durant, Éloi Monat, Cécile Rouard, Mathieu Hu, Haifei Chapman, Brett Li, Chengdao Cheng, Shifeng Batley, Jacqueline Edwards, David |
| author_browse | Batley, Jacqueline Bayer, Philipp E. Chapman, Brett Cheng, Shifeng Durant, Éloi Edwards, David Hu, Haifei Li, Chengdao Monat, Cécile Petereit, Jakob Rouard, Mathieu |
| author_facet | Bayer, Philipp E. Petereit, Jakob Durant, Éloi Monat, Cécile Rouard, Mathieu Hu, Haifei Chapman, Brett Li, Chengdao Cheng, Shifeng Batley, Jacqueline Edwards, David |
| author_sort | Bayer, Philipp E. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes. |
| format | Journal Article |
| id | CGSpace119697 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1196972025-11-11T17:44:30Z Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome Bayer, Philipp E. Petereit, Jakob Durant, Éloi Monat, Cécile Rouard, Mathieu Hu, Haifei Chapman, Brett Li, Chengdao Cheng, Shifeng Batley, Jacqueline Edwards, David genomes genetic databases varieties genomas base de datos de recursos genéticos variedades genetics Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes. 2022-09 2022-05-31T10:43:23Z 2022-05-31T10:43:23Z Journal Article https://hdl.handle.net/10568/119697 en Open Access application/pdf Wiley Bayer, P.E.; Petereit, J.; Durant, É.; Monat, C.; Rouard, M.; Hu, H.; Chapman, B.; Li, C.; Cheng, S.; Batley, J.; Edwards, D. (2022) Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome. The Plant Genome, Online first paper (29 May 2022). ISSN: 1940-3372 |
| spellingShingle | genomes genetic databases varieties genomas base de datos de recursos genéticos variedades genetics Bayer, Philipp E. Petereit, Jakob Durant, Éloi Monat, Cécile Rouard, Mathieu Hu, Haifei Chapman, Brett Li, Chengdao Cheng, Shifeng Batley, Jacqueline Edwards, David Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title | Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title_full | Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title_fullStr | Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title_full_unstemmed | Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title_short | Wheat Panache: A pangenome graph database representing presence–absence variation across sixteen bread wheat genome |
| title_sort | wheat panache a pangenome graph database representing presence absence variation across sixteen bread wheat genome |
| topic | genomes genetic databases varieties genomas base de datos de recursos genéticos variedades genetics |
| url | https://hdl.handle.net/10568/119697 |
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