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Plant Cell Physiol. 2016 Jan;57(1):e1. doi: 10.1093/pcp/pcv171. Epub 2015 Nov 16.

OryzaGenome: Genome Diversity Database of Wild Oryza Species.

Author information

1
Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan Bioinformatics Laboratory, Meiji University, Kawasaki, Japan Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Japan Present address: Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
2
DYNACOM Co., Ltd., Chiba, Japan.
3
National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China.
4
Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan.
5
Genome Informatics Laboratory, National Institute of Genetics, Mishima, Japan.
6
Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.
7
Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.
8
Genome Informatics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.
9
Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan National Center for Gene Research, Chinese Academy of Sciences, Shanghai, PR China.
10
Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan nkurata@nig.ac.jp.

Abstract

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

KEYWORDS:

Database; Genome diversity; Genus Oryza; NGS; NIG Wild Rice Collection; Oryza rufipogon; Oryzabase; SNP

PMID:
26578696
PMCID:
PMC4722174
DOI:
10.1093/pcp/pcv171
[Indexed for MEDLINE]
Free PMC Article

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