气候变化领域集成服务门户(CCPortal): OryzaGenome: Genome Diversity Database of Wild Oryza Species

CCPortal

DOI	10.1093/pcp/pcv171
	OryzaGenome: Genome Diversity Database of Wild Oryza Species
	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
发表日期	2016
ISSN	0032-0781
EISSN	1471-9053
卷号	57 期号:1
英文摘要	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/.
关键词	Database Genome diversity Genus Oryza NIG Wild Rice Collection NGS Oryzabase Oryza rufipogon SNP
学科领域	Plant Sciences; Cell Biology
语种	英语
WOS研究方向	Plant Sciences ; Cell Biology
来源期刊	PLANT AND CELL PHYSIOLOGY
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111891
作者单位	Natl Inst Genet, Plant Genet Lab, Mishima, Shizuoka 411, Japan
推荐引用方式 GB/T 7714	Ohyanagi, Hajime,Ebata, Toshinobu,Huang, Xuehui,et al. OryzaGenome: Genome Diversity Database of Wild Oryza Species[J]. 中国科学院西北生态环境资源研究院,2016,57(1).
APA	Ohyanagi, Hajime.,Ebata, Toshinobu.,Huang, Xuehui.,Gong, Hao.,Fujita, Masahiro.,...&Kurata, Nori.(2016).OryzaGenome: Genome Diversity Database of Wild Oryza Species.PLANT AND CELL PHYSIOLOGY,57(1).
MLA	Ohyanagi, Hajime,et al."OryzaGenome: Genome Diversity Database of Wild Oryza Species".PLANT AND CELL PHYSIOLOGY 57.1(2016).