Through collaboration with the NSF-funded Oryza Genome Evolution (OGE) Project and others, the Gramene web portal is building a genus-level resource for comparative genomics in cultivated rice and their wild relatives. The site includes complete reference sequences and community annotations for the 3 cultivated species/subspecies: O. sativa ssp. japonica, O. sativa ssp. indica, and O. glaberrima (African rice). It also hosts a vertical data set of chromosome 3 short-arm assemblies of 8 species, comprised of progenitors of cultivated rice and several of the known Oryza genome types (including an allopolyploid): O. glaberrima (AA), O. barthii (AA), O. nivara (AA), O. rufipogon (AA), O. punctata (BB), O. minuta (BBCC), O. officinalis (CC), and O. brachyantha (FF). Each is displayed in a genome browser showing predicted gene models, repeats, and EST alignments. Ancestrally conserved regions and structural rearrangements are defined by whole-genome alignments and displayed in a number of informative ways, including a multi-species view that allows graphical stacking of browsers and interspecies navigation. A comprehensive set of gene families and interactive phylogenetic trees were built using a method that performs taxonomic dating of gene duplication events and prediction of orthologs and paralogs. Over the course of the OGE Project Gramene will expand to include additional Oryza genomes, population and expression data. This resource will strengthen the research community as it seeks to resolve questions about the evolution of the Oryza genus, elucidate gene structure and function, and identify targets for future agronomic improvement of rice.
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