Martin, Joel A
Duong, Phat Q
Pham, Nikki T
Kudrna, David A
Schackwitz, Wendy S
Lipzen, Anna M
Nelson, Catherine R
Barry, Kerrie W
Wing, Rod A
Ronald, Pamela C
AffiliationUniv Arizona, Sch Plant Sci, Arizona Genom Inst
Univ Arizona, Sch Plant Sci, Inst BIO5
KeywordsDe novo genome assembly
Whole genome sequence
XA21 immune receptor
MetadataShow full item record
CitationJain, R., Jenkins, J., Shu, S. et al. Genome sequence of the model rice variety KitaakeX. BMC Genomics 20, 905 (2019). https://doi.org/10.1186/s12864-019-6262-4
RightsCopyright © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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AbstractBackground 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.
NoteOpen access journal
VersionFinal published version
SponsorsNIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [GM122968, GM59962]; NSFNational Science Foundation (NSF) [IOS-1237975]; U.S. Department of Energy, Office of Science, Office of Biological and Environmental ResearchUnited States Department of Energy (DOE) [DE-AC02-05CH11231]
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