OryzaGenome: Genome Diversity Database of Wild Oryza Species

Handle URI:
http://hdl.handle.net/10754/622355
Title:
OryzaGenome: Genome Diversity Database of Wild Oryza Species
Authors:
Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi Xuan; Han, Bin; Kurata, Nori
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 textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited 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/.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Ohyanagi H, Ebata T, Huang X, Gong H, Fujita M, et al. (2015) OryzaGenome: Genome Diversity Database of WildOryzaSpecies. Plant and Cell Physiology 57: e1–e1. Available: http://dx.doi.org/10.1093/pcp/pcv171.
Publisher:
Oxford University Press (OUP)
Journal:
Plant and Cell Physiology
Issue Date:
18-Nov-2015
DOI:
10.1093/pcp/pcv171
Type:
Article
ISSN:
0032-0781; 1471-9053
Sponsors:
This work was supported by the National BioResource Project (NBRP) [the Genome Information Upgrading Program to (N.K. and A.T.)]; the Genetic Function Systems Project in the Transdisciplinary Research Integration Center at Research Organization of Information and Systems (TRIC/ROIS) [to N.K. and A.F.].
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorEbata, Toshinobuen
dc.contributor.authorHuang, Xuehuien
dc.contributor.authorGong, Haoen
dc.contributor.authorFujita, Masahiroen
dc.contributor.authorMochizuki, Takakoen
dc.contributor.authorToyoda, Atsushien
dc.contributor.authorFujiyama, Asaoen
dc.contributor.authorKaminuma, Elien
dc.contributor.authorNakamura, Yasukazuen
dc.contributor.authorFeng, Qien
dc.contributor.authorWang, Zi Xuanen
dc.contributor.authorHan, Binen
dc.contributor.authorKurata, Norien
dc.date.accessioned2017-01-02T09:28:26Z-
dc.date.available2017-01-02T09:28:26Z-
dc.date.issued2015-11-18en
dc.identifier.citationOhyanagi H, Ebata T, Huang X, Gong H, Fujita M, et al. (2015) OryzaGenome: Genome Diversity Database of WildOryzaSpecies. Plant and Cell Physiology 57: e1–e1. Available: http://dx.doi.org/10.1093/pcp/pcv171.en
dc.identifier.issn0032-0781en
dc.identifier.issn1471-9053en
dc.identifier.doi10.1093/pcp/pcv171en
dc.identifier.urihttp://hdl.handle.net/10754/622355-
dc.description.abstractThe 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 textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited 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/.en
dc.description.sponsorshipThis work was supported by the National BioResource Project (NBRP) [the Genome Information Upgrading Program to (N.K. and A.T.)]; the Genetic Function Systems Project in the Transdisciplinary Research Integration Center at Research Organization of Information and Systems (TRIC/ROIS) [to N.K. and A.F.].en
dc.publisherOxford University Press (OUP)en
dc.subjectDatabaseen
dc.subjectGenome diversityen
dc.subjectGenus Oryzaen
dc.subjectNGSen
dc.subjectNIG Wild Rice Collectionen
dc.subjectOryza rufipogonen
dc.subjectOryzabaseen
dc.subjectSNPen
dc.titleOryzaGenome: Genome Diversity Database of Wild Oryza Speciesen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPlant and Cell Physiologyen
dc.contributor.institutionPlant Genetics Laboratory, National Institute of Genetics, Mishima, Japanen
dc.contributor.institutionBioinformatics Laboratory, Meiji University, Kawasaki, Japanen
dc.contributor.institutionTsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Japanen
dc.contributor.institutionDYNACOM Co., Ltd., Chiba, Japanen
dc.contributor.institutionNational Center for Gene Research, Chinese Academy of Sciences, Shanghai, Chinaen
dc.contributor.institutionGenome Informatics Laboratory, National Institute of Genetics, Mishima, Japanen
dc.contributor.institutionComparative Genomics Laboratory, National Institute of Genetics, Mishima, Japanen
dc.contributor.institutionDepartment of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japanen
kaust.authorOhyanagi, Hajimeen
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