Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes
Abstract Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes...
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| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20535 |
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| author | Tessa R. MacNish Hawlader A. Al‐Mamun Philipp E. Bayer Connor McPhan Cassandria G. Tay Fernandez Shriprabha R. Upadhyaya Shengyi Liu Jacqueline Batley Isobel A. P. Parkin Andrew G. Sharpe David Edwards |
| author_facet | Tessa R. MacNish Hawlader A. Al‐Mamun Philipp E. Bayer Connor McPhan Cassandria G. Tay Fernandez Shriprabha R. Upadhyaya Shengyi Liu Jacqueline Batley Isobel A. P. Parkin Andrew G. Sharpe David Edwards |
| author_sort | Tessa R. MacNish |
| collection | DOAJ |
| description | Abstract Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi‐species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache). |
| format | Article |
| id | doaj-art-047da1dbf6cd4690b521d82f924cc5ca |
| institution | Kabale University |
| issn | 1940-3372 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-047da1dbf6cd4690b521d82f924cc5ca2025-08-20T03:43:57ZengWileyThe Plant Genome1940-33722025-03-01181n/an/a10.1002/tpg2.20535Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomesTessa R. MacNish0Hawlader A. Al‐Mamun1Philipp E. Bayer2Connor McPhan3Cassandria G. Tay Fernandez4Shriprabha R. Upadhyaya5Shengyi Liu6Jacqueline Batley7Isobel A. P. Parkin8Andrew G. Sharpe9David Edwards10School of Biological Sciences The University of Western Australia Perth Western Australia AustraliaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaOil Crops Research Institute, CAAS Wuhan ChinaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaAgriculture and Agri‐Food Canada Saskatoon Saskatchewan CanadaGlobal Institute for Food Security Saskatoon Saskatchewan CanadaSchool of Biological Sciences The University of Western Australia Perth Western Australia AustraliaAbstract Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi‐species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache).https://doi.org/10.1002/tpg2.20535 |
| spellingShingle | Tessa R. MacNish Hawlader A. Al‐Mamun Philipp E. Bayer Connor McPhan Cassandria G. Tay Fernandez Shriprabha R. Upadhyaya Shengyi Liu Jacqueline Batley Isobel A. P. Parkin Andrew G. Sharpe David Edwards Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes The Plant Genome |
| title | Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes |
| title_full | Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes |
| title_fullStr | Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes |
| title_full_unstemmed | Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes |
| title_short | Brassica Panache: A multi‐species graph pangenome representing presence absence variation across forty‐one Brassica genomes |
| title_sort | brassica panache a multi species graph pangenome representing presence absence variation across forty one brassica genomes |
| url | https://doi.org/10.1002/tpg2.20535 |
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