About OryzaGenome

OryzaGenome is planed to provide genome sequence information for 21 wild Oryza species together with several species/accessions reference sequences. As of the OryzaGenome release 1.0 (on June 19, 2015), SNP information of 446 accessions of O. rufipogon is presented. Chromosome view, genome sequences and gene annotations are provided based on the latest reference Nipponbare genome, IRGSP version 1.0.

We will build and release pseudo-molecules and genome–wide variation information for additional 20 wild Oryza species accessions using NIG/NBRP collection (about 200 accessions) as the release 3.0 following the present release 2.0 open here. Construction, maintenance and release of the OryzaGenome is fully supported by the National BioResource Project, Japan (NBRP) and the National Institute of Genetics.

Release 2.0 contents

Oryza 200 Genome project has released the genome sequence data of 208 accessions from 19 wild and 2 cultivated Oryza species collected in the National Institute of Genetics Japan and a part from other institutions for comparison. All accession has sequence information of illumina short reads (100-150 bp) of over x10 depth of each genome length. Each sequence data has registered as available DRA information in the DDBJ. The DRA number information is linked from the table of the release 2.0. Detailed information and related analysis data will be open to the public soon after manuscript acceptance.

Release 2.0 contains fully developed information of SNP Table to search and select SNPs with specific characteristics. The SNP table can be exported to a CSV format and then imported into Excel or another application that can read CSV files. SNP Viewer annotation track identifies regions subject to selective sweeps and regions of high differentiation in O.rufipogon population (Haung et al., 2012). As the basis of GWA analysis for wild O.rufipogon accessions, phyenotypic, metabolomic and non-missing genotypes data will be provided.

Release 1.0 contents

• 17 deep NGS genome sequences comprising eleven O. rufipogon accessions and two O. longistaminata accessions (W1413 and W1508) resequenced at 10x〜20x depth, mapped and each covering about 80-90% of the genome are shown (performed by the NIG group and will be published soon). Three cultivated strains: O. sativa, japonica, Nipponbare (NIG stock), indica, Guangluai-4 and japonica, Nongken-58 sequenced in our previous work [1], and one more cultivar, the Aus-type Kasalat sequenced by Sakai et al [2], were also mapped and aligned for reference.
• Low coverage data of 446 accessions of O. rufipogon, the direct ancestors of cultivated rice O. sativa, were incorporated from our publication [1] and re-mapped onto IRGSP ver1.0. Although most of the 446 wild accessions were sequenced at only about 1x genome depth covering less than 10% of the genome, based on the mapped sequences of all 446 accessions, SNPs were imputed (method reported in [3]) and reconstructed about 30% of the genome of each accession (SNPs located at 200bp intervals on average). These imputed SNPs were proven to show high accuracy, with a probability of more than 98%. The raw data of illumina Hi-seq2000 genome reads for each accession can be retrieved from the archives with the indicated DRR, DRA or ERA numbers in the accession list.
• References
  • [1] Huang et al. Nature 490; 497 - 501 (2012)
  • [2] Sakai et al., DNA Res. 21; 397 - 405 (2014)
  • [3] Huang et al., Nature Genet. 42; 961 - 967 (2010)

Acknowledgements

Datasets provided here are collected mainly from the wild Oryza species maintained in the National Institute of Genetics (NIG) under the National Bioresource Project (NBRP). We also thank the Genetic Function Systems Project in TRIC/ROIS and the Project for Promotion of Next-Generation Genome Research Network, NIGfor supporting the preservation of wild accessions, sequencing, data analysis and database construction. We are grateful to Mr Toshinobu Ebata and Dynacom Co. Ltd., for constructing the OryzaGenome database.