Статья

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

Yoshihiro KawaharaAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan. [email protected]M. de la BastideCold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, NY, 11723, USAJohn P. HamiltonDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USAHiroyuki KanamoriAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanW. Richard McCombieCold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, NY, 11723, USAShu OuyangPerkin Elmer, Room 4096, 8490 Progress Drive, Frederick, MD, 21701, USADavid C. SchwartzLaboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI, 53706, USATsuyoshi TanakaAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanJianzhong WuAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanShiguo ZhouLaboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, UW-Biotechnology Center, 425 Henry Mall, Madison, WI, 53706, USAKevin L. ChildsDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USARebecca M. DavidsonDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USAHaining LinDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USAL. M. Quesada-OcampoDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USABrieanne VaillancourtDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USAHiroaki SakaiAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanSung Shin LeeAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanJungsok KimAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanHisataka NumaAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanTakeshi ItohAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, JapanC. Robin BuellDepartment of Plant Biology, Michigan State University, Plant Biology Laboratories, 612 Wilson Rd, East Lansing, MI, 48824, USATakashi MatsumotoAgrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan

2013en

ABI

Аннотация

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.

Перевод пока недоступен

Идентификаторы

DOI: 10.1186/1939-8433-6-4

Цитирования и источники

Цитирований: 2Использованных источников: 0

Показатели — AkademScholar