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Title: Genome sequence of the model rice variety KitaakeX

Abstract

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 acceleratemore » 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.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1618575
Alternate Identifier(s):
OSTI ID: 1582348
Grant/Contract Number:  
AC02-05CH11231; GM59962; GM122968; IOS-1237975
Resource Type:
Published Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Name: BMC Genomics Journal Volume: 20 Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer Science + Business Media
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Rice; Kitaake; KitaakeX; XA21 immune receptor; Whole genome sequence; De novo genome assembly; Nipponbare; Zhenshan97

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 Kingdom: N. p., 2019. Web. https://doi.org/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 Kingdom. https://doi.org/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 Kingdom. https://doi.org/10.1186/s12864-019-6262-4.
@article{osti_1618575,
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 = {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 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 Kingdom},
year = {2019},
month = {11}
}

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https://doi.org/10.1186/s12864-019-6262-4

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