Kajiya-Kanegae Hiromi, Ohyanagi Hajime, Ebata Toshinobu, Tanizawa Yasuhiro, Onogi Akio, Sawada Yuji, Hirai Masami Yokota, Wang Zi-Xuan, Han Bin, Toyoda Atsushi, Fujiyama Asao, Iwata Hiroyoshi, Tsuda Katsutoshi, Suzuki Toshiya, Nosaka-Takahashi Misuzu, Nonomura Ken-Ichi, Nakamura Yasukazu, Kawamoto Shoko, Kurata Nori, Sato Yutaka
Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo 1-1-1, Tokyo, 113-8657, Japan.
King Abdullah University of Science and Technology, Computational Bioscience Research Center, Biological and Environmental Sciences & Engineering Division, Thuwal, 23955-6900, Saudi Arabia.
Rice (N Y). 2021 Mar 4;14(1):24. doi: 10.1186/s12284-021-00468-x.
OryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.xhtml ), a feature within Oryzabase ( https://shigen.nig.ac.jp/rice/oryzabase/ ), is a genomic database for wild Oryza species that provides comparative and evolutionary genomics approaches for the rice research community.
Here we release OryzaGenome2.1, the first major update of OryzaGenome. The main feature in this version is the inclusion of newly sequenced genotypes and their meta-information, giving a total of 217 accessions of 19 wild Oryza species (O. rufipogon, O. barthii, O. longistaminata, O. meridionalis, O. glumaepatula, O. punctata, O. minuta, O. officinalis, O. rhizomatis, O. eichingeri, O. latifolia, O. alta, O. grandiglumis, O. australiensis, O. brachyantha, O. granulata, O. meyeriana, O. ridleyi, and O. longiglumis). These 19 wild species belong to 9 genome types (AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ), representing wide genomic diversity in the genus. Using the genotype information, we analyzed the genome diversity of Oryza species. Other features of OryzaGenome facilitate the use of information on single nucleotide polymorphisms (SNPs) between O. sativa and its wild progenitor O. rufipogon in rice research, including breeding as well as basic science. For example, we provide Variant Call Format (VCF) files for genome-wide SNPs of 33 O. rufipogon accessions against the O. sativa reference genome, IRGSP1.0. In addition, we provide a new SNP Effect Table function, allowing users to identify SNPs or small insertion/deletion polymorphisms in the 33 O. rufipogon accessions and to search for the effect of these polymorphisms on protein function if they reside in the coding region (e.g., are missense or nonsense mutations). Furthermore, the SNP Viewer for 446 O. rufipogon accessions was updated by implementing new tracks for possible selective sweep regions and highly mutated regions that were potentially exposed to selective pressures during the process of domestication.
OryzaGenome2.1 focuses on comparative genomic analysis of diverse wild Oryza accessions collected around the world and on the development of resources to speed up the identification of critical trait-related genes, especially from O. rufipogon. It aims to promote the use of genotype information from wild accessions in rice breeding and potential future crop improvements. Diverse genotypes will be a key resource for evolutionary studies in Oryza, including polyploid biology.
在此，我们发布OryzaGenome2.1，这是OryzaGenome的首次重大更新。该版本的主要特点是纳入了新测序的基因型及其元信息，共有19种野生稻种（普通野生稻、非洲栽培稻、长花药野生稻、南方野生稻、阔叶野生稻、斑点野生稻、小粒野生稻、药用野生稻、瘤粒野生稻、展颖野生稻、宽叶野生稻、高杆野生稻、大颖野生稻、澳洲野生稻、短药野生稻、疣粒野生稻、长喙毛茛泽泻、长颖野生稻）的217份种质。这19种野生稻属于9种基因组类型（AA、BB、CC、BBCC、CCDD、EE、FF、GG和HHJJ），代表了该属广泛的基因组多样性。利用基因型信息，我们分析了稻种的基因组多样性。OryzaGenome的其他功能有助于在水稻研究（包括育种和基础科学）中利用栽培稻及其野生祖先普通野生稻之间的单核苷酸多态性（SNP）信息。例如，我们提供了33份普通野生稻种质相对于栽培稻参考基因组IRGSP1.0的全基因组SNP的变异调用格式（VCF）文件。此外，我们提供了一个新的SNP效应表功能，允许用户识别33份普通野生稻种质中的SNP或小插入/缺失多态性，并搜索这些多态性对蛋白质功能的影响（例如，是否为错义或无义突变）。此外，通过为可能的选择清除区域和驯化过程中可能受到选择压力的高突变区域实施新的轨迹，更新了446份普通野生稻种质的SNP查看器。
OryzaGenome2.1专注于对世界各地收集的不同野生稻种质进行比较基因组分析，并致力于开发资源以加速关键性状相关基因的鉴定，特别是来自普通野生稻的基因。它旨在促进野生种质的基因型信息在水稻育种以及未来潜在作物改良中的应用。多样的基因型将是水稻进化研究（包括多倍体生物学）的关键资源。
