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.

doi:10.1186/s12864-019-6262-4

Genome sequence of the model rice variety KitaakeX

Journal Article · Wed Nov 27 00:00:00 EST 2019 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-019-6262-4· OSTI ID:1618575

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. more »

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618575

Alternate ID(s):: OSTI ID: 1582348

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 20; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
De novo genome assembly
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XA21 immune receptor
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