Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data

Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., Itoh, T., Buell, C. R., Matsumoto, T. (2013) Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice, 6 (1). pp. 3-10. ISSN 19398425 (ISSN)

[img]
Preview
PDF (Paper)
McCombie Rice Journal 2013.pdf - Published Version

Download (546Kb) | Preview
URL: https://www.ncbi.nlm.nih.gov/pubmed/24280374
DOI: 10.1186/1939-8433-6-4

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.

Item Type: Paper
Uncontrolled Keywords: Genome re-sequencing Minimum tiling path Next-generation sequencing Nipponbare Optical mapping Oryza sativa Pseudomolecules Unified rice reference genome
Subjects: bioinformatics > genomics and proteomics > alignment
bioinformatics > genomics and proteomics > annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
organism description > plant > rice
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: Matt Covey
Date Deposited: 25 Apr 2013 13:46
Last Modified: 05 Dec 2016 21:25
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28226

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving