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Title: Genome sequence of the model rice variety KitaakeX

Abstract

BACKGROUND: 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 ricemore » functional genomics.CONCLUSIONS: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.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1582348
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English

Citation Formats

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. Genome sequence of the model rice variety KitaakeX. United States: N. p., 2019. Web. doi:10.1186/s12864-019-6262-4.
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. United States. doi:10.1186/s12864-019-6262-4.
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. Wed . "Genome sequence of the model rice variety KitaakeX". United States. doi:10.1186/s12864-019-6262-4. https://www.osti.gov/servlets/purl/1582348.
@article{osti_1582348,
title = {Genome sequence of the model rice variety KitaakeX},
author = {Jain, Rashmi and Jenkins, Jerry and Shu, Shengqiang and Chern, Mawsheng and Martin, Joel A. and Copetti, Dario and Duong, Phat Q. and Pham, Nikki T. and Kudrna, David A. and Talag, Jayson and Schackwitz, Wendy S. and Lipzen, Anna M. and Dilworth, David and Bauer, Diane and Grimwood, Jane and Nelson, Catherine R. and Xing, Feng and Xie, Weibo and Barry, Kerrie W. and Wing, Rod A. and Schmutz, Jeremy and Li, Guotian and Ronald, Pamela C.},
abstractNote = {BACKGROUND: 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.CONCLUSIONS: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.},
doi = {10.1186/s12864-019-6262-4},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {11}
}

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