Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data Yoshihiro Kawahara, Melissa de la Bastide, John P Hamilton, Hiroyuki Kanamori, W Richard McCombie, Shu Ouyang, David C Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou, Kevin L Childs, Rebecca M Davidson, Haining Lin, Lina Quesada-Ocampo, Brieanne Vaillancourt, Hiroaki Sakai, Sung Shin Lee, Jungsok Kim, Hisataka Numa, Takeshi ItohEmail author, C Robin Buell and Takashi Matsumoto Rice20136:4 DOI: 10.1186/1939-8433-6-4 © Kawahara et al.; licensee Springer. 2013 Received: 6 November 2012 Accepted: 30 January 2013 Published: 6 February 2013

An Oryza sativa culivar that is an updated assembly of "Os-Nipponbare-Reference-IRGSP-1.0" signifying that it is from rice (Oryza sativa), the Nipponbare cultivar, a high quality reference assembly, from the IRGSP, and version 1.0. We envision that future assemblies of rice will be of draft quality and from other entities, and as is the case with the Nipponbare rice genome, will be updated as new sequencing datasets become available in the future. We are proposing this nomenclature for other rice genome assemblies as an informative way for the community to readily interpret the origin, quality, and iteration of rice genome sequences. One objective in this study was to provide a single unified set of pseudomolecules for two parallel annotation efforts, the RAP (Tanaka et al. 2008, http://​rapdb.​dna.​affrc.​go.​jp/​) and the MSU Rice Genome Annotation Project (Ouyang et al. 2007, http://​rice.​plantbiology.​msu.​edu/​) in which both annotation projects have now updated their annotation with the underlying Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and provided this via their project websites.

http://thericejournal.springeropen.com/articles/10.1186/1939-8433-6-4

Oryza sativa Nipponbare, Nipponbare, Oryza sativa, Nipponbare, Oryza sativa cultivar Nipponbare

Sirarat Sarntivijai