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Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Yoshihiro Kawahara1, Melissa de la Bastide2, John P Hamilton3, Hiroyuki Kanamori1, W Richard McCombie2, Shu Ouyang4, David C Schwartz5, Tsuyoshi Tanaka1, Jianzhong Wu1, Shiguo Zhou5, Kevin L Childs3, Rebecca M Davidson36, Haining Lin37, Lina Quesada-Ocampo3, Brieanne Vaillancourt3, Hiroaki Sakai1, Sung Shin Lee1, Jungsok Kim1, Hisataka Numa1, Takeshi Itoh1*, C Robin Buell3 and Takashi Matsumoto1

Author Affiliations

1 Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

2 Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, NY, 11723, USA

3 Department of Plant Biology, Michigan State University, 612 Wilson Rd, Plant Biology Laboratories, East Lansing, MI, 48824, USA

4 Perkin Elmer, Room 4096, 8490 Progress Drive, Frederick, MD, 21701, USA

5 Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI, 53706, USA

6 Integrated Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA

7 Dupont Pioneer, 7200 NW 62nd Ave, Johnston, IA, 50131, USA

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Rice 2013, 6:4  doi:10.1186/1939-8433-6-4

Published: 6 February 2013



Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).


The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.


A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.

Oryza sativa; Nipponbare; Unified rice reference genome; Pseudomolecules; Minimum tiling path; Optical mapping; Genome re-sequencing; Next-generation sequencing