RRC ID 36322
著者 Ohyanagi H, Ebata T, Huang X, Gong H, Fujita M, Mochizuki T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y, Feng Q, Wang ZX, Han B, Kurata N.
タイトル OryzaGenome: Genome Diversity Database of Wild Oryza Species.
ジャーナル Plant Cell Physiol
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/.
巻・号 57(1)
ページ e1
公開日 2016-1-1
DOI 10.1093/pcp/pcv171
PII pcv171
PMID 26578696
PMC PMC4722174
MeSH Databases, Genetic* Genetic Variation* Genome, Plant / genetics* Genomics* Genotype Oryza / genetics* Phenotype Polymorphism, Single Nucleotide
IF 4.062
引用数 17
WOS 分野 PLANT SCIENCES CELL BIOLOGY
リソース情報
イネ
情報 Oryzabase