OryzaGenome: Genome Diversity Database of Wild Oryza Species.
OryzaGenome: Genome Diversity Database of Wild Oryza Species.
复制标题
DOI：
10.1093/pcp/pcv171
复制
发表时间：
2016-01
影响因子：
4.9
通讯作者：
Kurata N
中科院分区：
文献类型：
--
作者：
Ohyanagi H;Ebata T;Huang X;Gong H;Fujita M;Mochizuki T;Toyoda A;Fujiyama A;Kaminuma E;Nakamura Y;Feng Q;Wang ZX;Han B;Kurata N
稻属物种包含 9 种基因组类型和 23 个物种，是丰富的遗传资源，可能在旨在了解植物基因组进化的更深入的基因组分析中得到应用。近年来，随着新一代测序（NGS）技术的进步，大量水稻物种参考基因组和基因组变异信息已成为可用。这些基因组信息与我们在 Oryzabase 中积累的全面表型信息相结合，可以作为分析水稻功能和结构进化以及稻属相关多样性的优秀基因型-表型关联资源。在这里，我们将以前和未来的表型/栖息地信息和新确定的基因型信息整合到一个名为 OryzaGenome 的联合存储库中，提供带有 Oryzabase 超链接的变异信息。当前版本的 OryzaGenome 包括通过插补获得的 446 个普通野生稻种质和通过无插补深度测序获得的 17 个种质的基因型信息。实现了两种变体查看器：SNP Viewer 作为传统的基因组浏览器界面，Variant Table 作为基于文本的浏览器，用于逐个精确检查每个变体。还提供便携式 VCF（变体调用格式）文件或制表符分隔文件下载。根据这些 SNP（单核苷酸多态性）数据，NIG 野生稻收藏中几乎所有近缘和远缘野生稻物种的参考假分子/支架/重叠群和全基因组变异信息将在未来版本中提供。所有资源都可以通过http://viewer.shigen.info/oryzagenome/访问。
The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype–phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.