Abstract
BackgroundRice 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).ResultsThe 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.ConclusionsA 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.
Highlights
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 distinguish allelic differences between the genome sequence and the National Institute of Agrobiological Sciences (NIAS) and Cold Spring Harbor Laboratory (CSHL) re-sequenced individuals, we examined three datasets, NIAS, CSHL, and NIAS + CSHL, that had average read depths of 7.9, 35.7, and 43.6, respectively
Our survey of alleles found variations within the Nipponbare cultivar that are mostly attributable to outcrossing, residual heterozygosity, and/or somatic mutations through the standard process of propagation in individual laboratories
Summary
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 International Rice Genome Sequencing Project (IRGSP) completed the sequencing of the japonica rice cultivar Nipponbare in 2005 (International Rice Genome Sequencing Project 2005). In this project, the consortium employed a clone-by-clone sequencing strategy after construction of a minimum tiling path (MTP) for each chromosome. A unified, single genome assembly of the Nipponbare rice reference genome was constructed by updating the MTP, validating the final MTP with optical mapping data, and error-correcting the unified assembly using generation re-sequencing data
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