Background

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.

Results

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.

Conclusion

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.

中文翻译：

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OryzaGenome2.1：野生稻种中不同基因型的数据库

背景

OryzaGenome（http://viewer.shigen.info/oryzagenome21detail/index.xhtml）是Oryzabase（https://shigen.nig.ac.jp/rice/oryzabase/）的一项功能，是野生Oryza物种的基因组数据库。为水稻研究界提供了比较和进化的基因组学方法。

结果

在这里，我们发布OryzaGenome2.1，这是OryzaGenome的第一个主要更新。在这个版本的主要特征是新测序的基因型和他们的元信息的纳入，共提供19个野生种质217稻品种（野生稻，O. barthii，O. longistaminata，O.鲇，O. glumaepatula，O. punctata，O. minuta，O. officinalis，O. rhizomatis，O. eichingeri，O. latifolia，O. alta，O. grandiglumis，O. australiensis，O. brachyantha，O. granulata，疣粒野生稻，O. ridleyi和O. longiglumis）。这19种野生物种属于9个基因组类型（AA，BB，CC，BBCC，CCDD，EE，FF，GG和HHJJ），代表该属中的广泛基因组多样性。利用基因型信息，我们分析了稻属物种的基因组多样性。OryzaGenome的其他功能，方便使用的单间核苷酸多态性（SNP）的信息栽培稻和野生祖先普通野生稻在水稻研究，包括育种，以及基础科学。例如，我们提供了针对33个O. rufipogon保藏号的全基因组单核苷酸多态性（SNP）的变异调用格式（VCF）文件。水稻参考基因组IRGSP1.0。此外，我们提供了新的SNP效果表功能，允许用户识别33个红景天种质中的SNP或小的插入/缺失多态性，并搜索这些多态性对蛋白质功能的影响（如果它们位于编码区中）（例如错义或无义突变）。此外，通过对可能的选择性扫描区域和高度变异的区域实施新的跟踪，更新了446个红景天种子的SNP Viewer，在驯化过程中它们可能会承受选择性的压力。

结论

OryzaGenome2.1专注于在世界范围内收集的各种野生Oryza品种的比较基因组分析，并致力于开发资源以加快关键性状相关基因的鉴定，特别是来自红景天。它的目的是促进野生品种的基因型信息在水稻育种中的应用以及未来作物的改良。不同的基因型将成为Oryza进化研究（包括多倍体生物学）的重要资源。