These 19 wild species belong to 9 genome types , 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 . 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.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 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.OryzaGenome2.1 focuses on comparative genomic analysis of diverse wild The online version contains supplementary material available at 10.1186/s12284-021-00468-x. Oryza species into cultivated rice species, with the aim of exploiting agronomically advantageous traits from diverse wild relatives.Rice is an essential food for humankind, playing a critical role in food security. In addition, rice is a well-established model monocot in plant science, enabling advanced genomic breeding approaches for rapid development of improved cultivars. One such approach is genomic introgression from either closely or distantly related wild Oryza sativa L.) genotypes have been made available to the public , a major update. This release features newly sequenced genotypes and their meta-information, for a total of 217 wild Oryza accessions from 19 Oryza species  as a reference genome sequence  following the instruction of the software   . Variants were called by HaplotypeCaller of the Genome Analysis Toolkit   files are accessible from the Downloads page Fig. . The anahttp://viewer.shigen.info/oryzagenome/mapview/VariantView.do?action=Downloads) was downloaded and re-imputed by beagle 4.0 software (Browning and Browning https://faculty.washington.edu/browning/beagle/b4_0.html). This file contains phased, non-missing genotypes for all non-reference positions and is available from the Downloads page.Imputed genome data were obtained as follows. Whole-genome information in OryzaGenome v. 1 Variant List , DataTables (https://www.datatables.net/), Magnific Popup (http://dimsemenov.com/plugins/magnific-popup/), Google chart tools (https://developers.google.com/chart/), Prototype (http://prototypejs.org/), and script.aculo.us (https://script.aculo.us/) were used. Other conventional utilities for UNIX computing were installed on the server as necessary. All the OryzaGenome2.1 resources are stored on the server and are available at http://viewer.shigen.info/oryzagenome21detail/index.xhtml.Java and C++ were used as server-side application languages. JavaScript was used to implement client-side rich applications. The JavaScript libraries jQuery (Oryza species (average coverage 18×) , and their variants against the japonica reference genome  217 Oryza Genotypes; (2) 33 O. rufipogon Genotypes and Variants; (3) SNP Viewer for 446 Imputed O. rufipogon Genotypess, with new information tracks; (4) SNP Effect Table function to search for the effects of variants in 33 O. rufipogon accessions against IRGSP1.0; and (5) Misc Downloads.OryzaGenome release 2.1 provides the genotypes of 217 highly diverse accessions from 19 wild Oryza species  are provided. The 19 wild species belong to 9 genome types , representing much more genomic divergence than in the previous version. Each accession has been genotyped by Illumina paired-end short-read DNA sequencing (100- to 150-bp read length for one end) of over 8× coverage (average 18× coverage). Users can browse the sequencing platform, total bases, coverage, and file size in a pop-up window by mouse-over action at the accession numbers that are hyperlinked to NCBI and DDBJ on the Downloads page -derived genotypes of 217 accessions from 19 wild age Fig.  describiOryza. K-mer analysis was conducted to estimate the size of genome, the content of repetitive sequences and the heterozygosity in the genome of each accession  for 33 accessions of O. rufipogon. The raw sequence data of these accessions, as well as VCF files containing information on variants against Os-Nipponbare-Reference-IRGSP-1.0, are provided on the Downloads page  is updated in this release. Chromosome coordinates, genome sequences, and gene annotations are based on the latest japonica reference genome, Os-Nipponbare-Reference-IRGSP-1.0 . The genomic coordinates show regions or loci that appear to have been exposed to particular selective pressures through the process of domestication. In addition to RAP-DB  was obtained by using the SnpEff tool  . BED-formatted annotations and Fst values for the 446 O. rufipogon accessions published in Huang et al.  as well as information on these 446 accessions including accession number, habitat/country of origin, ecotype, sequence coverage, and deposited IDs of NGS raw data.In OryzaGenome1, an initial set of imputation-derived variant information on 446 Oryza accessions. Most of the wild Oryza bioresources used for acquisition of genotype data in OryzaGenome are preserved at the National Institute of Genetics in Japan. These materials were collected during the 1950s to 1980s from around the world, and their biomaterials (such as seeds) are available from Oryzabase (https://shigen.nig.ac.jp/rice/oryzabase/) upon request. Thus, OryzaGenome will help to promote the use of wild Oryza bioresources in basic research and speed up the identification of critical agricultural-trait-related genes from these bioresources. OryzaGenome aims to promote rice breeding science as well as potential future crop improvement. OryzaGenome2.1 is a significant update, providing a genus-wide comprehensive genomic repository for wild Oryza species.The goal of OryzaGenome is to facilitate comparative and evolutionary genomic analysis of diverse wild O. rufipogon. For genes with known function, it is now possible to quickly narrow down SNPs linked to regions that may affect their function. Lists of SNPs in candidate regions can be quickly obtained on the web interface and downloaded as an Excel file.Improved web-based tools (the SNP Effect Table and SNP Viewer) allow visual inspection of SNPs of interest and the evolutionary background of the surrounding regions in Oryza genotypes, including newly sequenced genotypes of seven tetraploid Oryza species: O. minuta (BBCC), O. punctata (BBCC), O. alta (CCDD), O. grandiglumis (CCDD), O. latifolia (CCDD), O. longiglumis (HHJJ), and O. ridleyi (HHJJ). Compared with other comprehensive databases for Oryza genomics  and its wild progenitor (O. rufipogon) and to survey the effect of polymorphisms. These functions will contribute to the analysis of domestication processes and the identification of agriculturally important genes from wild progenitors.OryzaGenome2.1 provides access to a wide variety of Oryza genome information, such as OryzaGenome2.1, OMAP (http://www.omap.org/index.html), Gramene (http://www.gramene.org), Ensembl Plants (https://plants.ensembl.org/index.html), and Rice SNP seek (https://snp-seek.irri.org), will greatly facilitate evolutionary studies of Oryza and contribute to agricultural science. We also foresee that installing and integrating genome browsers for resequencing data, such as TASUKE+, in future versions of OryzaGenome will improve the user experience (Kumagai et al. We expect that cross-references between databases storing Additional file 1: Table S1. Accession list of OryzaGenome2.1.Additional file 2: Table S2. Summary of K-mer analysis using genotypes of 217 wild Oryza accessions.Additional file 3: Table S3 Number of homozygous small nucleotide polymorphisms in 33 O. rufipogon.Additional file 4: Fig. S1. Analysis of genome diversity among genus Oryza. A. A plot of estimated genome size and estimated repeat length among genus Oryza. B. A plot of estimated genome size and estimated repeat content among genus Oryza.