Genome sequence of the model rice variety KitaakeX
The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficienc...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2019
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| Acceso en línea: | https://hdl.handle.net/10568/164595 |
| _version_ | 1855516791028056064 |
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| author | Jain, Rashmi Jenkins, Jerry Shu, Shengqiang Chern, Mawsheng Martin, Joel A. Copetti, Dario Duong, Phat Q. Pham, Nikki T. Kudrna, David A. Talag, Jayson Schackwitz, Wendy S. Lipzen, Anna M. Dilworth, David Bauer, Diane Grimwood, Jane Nelson, Catherine R. Xing, Feng Xie, Weibo Barry, Kerrie W. Wing, Rod A. Schmutz, Jeremy Li, Guotian Ronald, Pamela C. |
| author_browse | Barry, Kerrie W. Bauer, Diane Chern, Mawsheng Copetti, Dario Dilworth, David Duong, Phat Q. Grimwood, Jane Jain, Rashmi Jenkins, Jerry Kudrna, David A. Li, Guotian Lipzen, Anna M. Martin, Joel A. Nelson, Catherine R. Pham, Nikki T. Ronald, Pamela C. Schackwitz, Wendy S. Schmutz, Jeremy Shu, Shengqiang Talag, Jayson Wing, Rod A. Xie, Weibo Xing, Feng |
| author_facet | Jain, Rashmi Jenkins, Jerry Shu, Shengqiang Chern, Mawsheng Martin, Joel A. Copetti, Dario Duong, Phat Q. Pham, Nikki T. Kudrna, David A. Talag, Jayson Schackwitz, Wendy S. Lipzen, Anna M. Dilworth, David Bauer, Diane Grimwood, Jane Nelson, Catherine R. Xing, Feng Xie, Weibo Barry, Kerrie W. Wing, Rod A. Schmutz, Jeremy Li, Guotian Ronald, Pamela C. |
| author_sort | Jain, Rashmi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species. |
| format | Journal Article |
| id | CGSpace164595 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1645952024-12-19T14:11:59Z Genome sequence of the model rice variety KitaakeX Jain, Rashmi Jenkins, Jerry Shu, Shengqiang Chern, Mawsheng Martin, Joel A. Copetti, Dario Duong, Phat Q. Pham, Nikki T. Kudrna, David A. Talag, Jayson Schackwitz, Wendy S. Lipzen, Anna M. Dilworth, David Bauer, Diane Grimwood, Jane Nelson, Catherine R. Xing, Feng Xie, Weibo Barry, Kerrie W. Wing, Rod A. Schmutz, Jeremy Li, Guotian Ronald, Pamela C. The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species. 2019-12 2024-12-19T12:54:06Z 2024-12-19T12:54:06Z Journal Article https://hdl.handle.net/10568/164595 en Open Access Springer Jain, Rashmi; Jenkins, Jerry; Shu, Shengqiang; Chern, Mawsheng; Martin, Joel A.; Copetti, Dario; Duong, Phat Q.; Pham, Nikki T.; Kudrna, David A.; Talag, Jayson; Schackwitz, Wendy S.; Lipzen, Anna M.; Dilworth, David; Bauer, Diane; Grimwood, Jane; Nelson, Catherine R.; Xing, Feng; Xie, Weibo; Barry, Kerrie W.; Wing, Rod A.; Schmutz, Jeremy; Li, Guotian and Ronald, Pamela C. 2019. Genome sequence of the model rice variety KitaakeX. BMC Genomics, Volume 20, no. 1 |
| spellingShingle | Jain, Rashmi Jenkins, Jerry Shu, Shengqiang Chern, Mawsheng Martin, Joel A. Copetti, Dario Duong, Phat Q. Pham, Nikki T. Kudrna, David A. Talag, Jayson Schackwitz, Wendy S. Lipzen, Anna M. Dilworth, David Bauer, Diane Grimwood, Jane Nelson, Catherine R. Xing, Feng Xie, Weibo Barry, Kerrie W. Wing, Rod A. Schmutz, Jeremy Li, Guotian Ronald, Pamela C. Genome sequence of the model rice variety KitaakeX |
| title | Genome sequence of the model rice variety KitaakeX |
| title_full | Genome sequence of the model rice variety KitaakeX |
| title_fullStr | Genome sequence of the model rice variety KitaakeX |
| title_full_unstemmed | Genome sequence of the model rice variety KitaakeX |
| title_short | Genome sequence of the model rice variety KitaakeX |
| title_sort | genome sequence of the model rice variety kitaakex |
| url | https://hdl.handle.net/10568/164595 |
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