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. 2013 Feb 6;6(1):4.
doi: 10.1186/1939-8433-6-4.

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

Yoshihiro Kawahara  1 , 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 Itoh, C Robin Buell, Takashi Matsumoto
Affiliations

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

Yoshihiro Kawahara et al. Rice (N Y). .

Abstract

Background: 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).

Results: 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.

Conclusions: 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.

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Figures

Figure 1
Figure 1
Depth of coverage of Illumina reads on the assembled genome. The depth of coverage of the Illumina reads at ≥1 read, ≥5 reads, and ≥10 reads are shown for the (A) NIAS, (B) CSHL, and (C) NIAS + CSHL datasets.
Figure 2
Figure 2
Frequency of allelic sites per 10 kb among the 12 rice chromosomes.
See this image and copyright information in PMC

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