Genome sequence of the model rice variety KitaakeX

Vista sencilla de ítem
dc.creatorJain, Rashmi
dc.creatorJenkins, Jerry
dc.creatorShu, Shengqiang
dc.creatorChern, Mawsheng
dc.creatorMartin, Joel A.
dc.creatorCopetti, Dario
dc.creatorDuong, Phat Q.
dc.creatorPham, Nikki T.
dc.creatorKudrna, David A.
dc.creatorTalag, Jayson
dc.creatorSchackwitz, Wendy S.
dc.creatorLipzen, Anna M.
dc.creatorDilworth, David
dc.creatorBauer, Diane
dc.creatorGrimwood, Jane
dc.creatorNelson, Catherine R.
dc.creatorXing, Feng
dc.creatorXie, Weibo
dc.creatorBarry, Kerrie W.
dc.creatorWing, Rod A.
dc.creatorSchmutz, Jeremy
dc.creatorLi, Guotian
dc.creatorRonald, Pamela C.
dc.date2019-12
dc.date2024-12-19T12:54:06Z
dc.date2024-12-19T12:54:06Z
dc.date.accessioned2026-06-27T04:08:17Z
dc.descriptionThe 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. 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.
dc.identifierhttps://hdl.handle.net/10568/164595
dc.identifier.urihttp://hdl.handle.net/123456789/22762
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceJain, 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. 2019. Genome sequence of the model rice variety KitaakeX. BMC Genomics, Volume 20, no. 1
dc.titleGenome sequence of the model rice variety KitaakeX
dc.typeJournal Article

Archivos

Colecciones

Instituto Internacional de Investigación del Arroz (IRRI)