About OryzaGenome

OryzaGenome is planned to provide genome sequence information for 21 wild Oryza species.

Release 2.1 contents

• A collection of Illumina paired-end short reads (100-150bp) over 10x depth from 217 accessions covering 19 Oryza species collected and maintained in National Institute of Genetics Japan including few accessions from other institution is released.
• New functions of 446 O. rufipogon acc. SNP viewer are equipped. Users can easily find highly differentiated loci and selective sweep reported in Huang et al., 2012, in addition, CGSNL gene nomenclature is presented.
• SNP Effect Table is renewed using new datasets of SNPs obtained from 33 deep sequenced O. rufipogon acc.
• vcf files for homozygous SNPs of 33 deep sequenced O. rufipogon acc. against IRGSP1.0 are released.

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 Kasalath 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, NIG for 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.