Title |
Genome sequence of the model rice variety KitaakeX
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Published in |
BMC Genomics, November 2019
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DOI | 10.1186/s12864-019-6262-4 |
Pubmed ID | |
Authors |
Rashmi Jain, Jerry Jenkins, Shengqiang Shu, Mawsheng Chern, Joel A. Martin, Dario Copetti, Phat Q. Duong, Nikki T. Pham, David A. Kudrna, Jayson Talag, Wendy S. Schackwitz, Anna M. Lipzen, David Dilworth, Diane Bauer, Jane Grimwood, Catherine R. Nelson, Feng Xing, Weibo Xie, Kerrie W. Barry, Rod A. Wing, Jeremy Schmutz, Guotian Li, Pamela C. Ronald |
Abstract |
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. 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 8 | 29% |
United Kingdom | 2 | 7% |
Australia | 2 | 7% |
Austria | 1 | 4% |
Canada | 1 | 4% |
Germany | 1 | 4% |
Vanuatu | 1 | 4% |
Netherlands | 1 | 4% |
Unknown | 11 | 39% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 15 | 54% |
Members of the public | 12 | 43% |
Science communicators (journalists, bloggers, editors) | 1 | 4% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 83 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 16 | 19% |
Student > Bachelor | 13 | 16% |
Student > Ph. D. Student | 13 | 16% |
Student > Master | 11 | 13% |
Student > Doctoral Student | 3 | 4% |
Other | 6 | 7% |
Unknown | 21 | 25% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 38 | 46% |
Biochemistry, Genetics and Molecular Biology | 17 | 20% |
Environmental Science | 2 | 2% |
Computer Science | 1 | 1% |
Social Sciences | 1 | 1% |
Other | 2 | 2% |
Unknown | 22 | 27% |