OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species.
Hirai, Masami Yokota
KAUST DepartmentBiological and Environmental Science and Engineering (BESE) Division
Online Publication Date2021-03-04
Print Publication Date2021-12
Permanent link to this recordhttp://hdl.handle.net/10754/667915
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AbstractBackgroundOryzaGenome ( 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.ResultsHere 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.ConclusionOryzaGenome2.1 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.
CitationKajiya-Kanegae, H., Ohyanagi, H., Ebata, T., Tanizawa, Y., Onogi, A., Sawada, Y., … Sato, Y. (2021). OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species. Rice, 14(1). doi:10.1186/s12284-021-00468-x
SponsorsWe thank the NBRP and NIG Bioresource Project for supporting the preservation of wild accessions and database construction. Some computations were performed on the NIG supercomputer at ROIS National Institute of Genetics. We acknowledge the support of Gaku Kimura, Hiroki Watanabe, and Rie Tsuchiya for web server management.
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