Wang, Zi Xuan
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Computational Bioscience Research Center (CBRC)
Online Publication Date2015-11-16
Print Publication Date2016-01
Embargo End Date2016-11-18
Permanent link to this recordhttp://hdl.handle.net/10754/622355
MetadataShow full item record
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/.
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.
SponsorsThis 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.].
PublisherOxford University Press (OUP)
JournalPlant and Cell Physiology
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