Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
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DOI：
10.1186/1939-8433-6-4
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发表时间：
2013-02-06
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影响因子：
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通讯作者：
Matsumoto T
中科院分区：
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作者：
Kawahara Y;de la Bastide M;Hamilton JP;Kanamori H;McCombie WR;Ouyang S;Schwartz DC;Tanaka T;Wu J;Zhou S;Childs KL;Davidson RM;Lin H;Quesada-Ocampo L;Vaillancourt B;Sakai H;Lee SS;Kim J;Numa H;Itoh T;Buell CR;Matsumoto T
通过获取国际水稻基因组测序计划 (IRGSP) 2005 年生成的高质量参考基因组序列，水稻研究得以实现。为了进一步促进基因组研究，我们更新并验证了日本晴稻品种（粳稻组）的基因组组装和序列。通过使用水稻光学图修改和验证克隆的最小平铺路径，更新了日本晴基因组组装。通过使用 Illumina Genome Analyzer II/IIx 平台对两个不同日本晴个体的基因组进行重新测序，确定了修订后的基因组组装中的测序错误。在 321 Mb 的组装基因组中总共鉴定出 4,886 个测序错误，表明原始 IRGSP 组装中的错误率仅为每 10,000 个核苷酸 0.15 个。使用 Roche 454 焦磷酸测序平台生成的较长读取来识别少量（五个）插入/缺失。由于重测序数据是从两个不同的个体生成的，因此我们能够识别 IRGSP 工作中使用的原始个体和重测序工作中使用的两个个体之间的许多等位基因差异。修订后的程序集被称为 Os-Nipponbare-Reference-IRGSP-1.0，目前用于水稻注释项目和密歇根州立大学水稻基因组注释项目的更新版本，从而为水稻界提供了一套统一的伪分子。使用光学图数据、重测序数据和手动管理生成了日本晴水稻品种的修订、纠错和验证组件，这将促进正在进行和未来的水稻研究。对三个不同日本晴个体之间多态性的检测强调，在多样性研究中应考虑个体之间的等位基因差异。本文的在线版本 (doi:10.1186/1939-8433-6-4) 包含补充材料，可供授权用户使用。
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. The online version of this article (doi:10.1186/1939-8433-6-4) contains supplementary material, which is available to authorized users.