Plant Comparative Genomics at Gramene
Apurva Narechania, Sharon Wei, William Spooner, Joshua C. Stein, Doreen Ware
Flowering plants underwent rapid diversification soon after their appearance in the fossil
record ~130 MYA and today play a dominant role in our terrestrial ecology. Multiple
rounds of whole genome duplication (polyploidy), with subsequent rearrangement, gene
loss and diversification characterize both the monocot and dicot lineages, and complicate
comparative genomics analyses. To ameliorate these complexities the Gramene Project
(www.gramene.org) has implemented the Ensembl Compara pipeline and database
structure. The resulting platform provides precomputed data resulting from whole
genome alignments, synteny analysis, phylogenetic trees, and orthologue/paralogue
designations, all accessible through the Gramene browser, with associated visualization
tools, comparative maps, and API. Recent updates include the genomes of three dicots
(Arabidopsis, grape, and poplar) and three monocots (rice, sorghum, and maize) which
are fully integrated with extensive gene and protein-level annotations, GO ontology, and
genetic maps. Orthologue/paralogue designation have also been extended to include
yeast, C. elegans, Drosophila, and humans. We describe details of this resource and
demonstrate its use in multiple applications, including the definition of both large and
small-scale rearrangements, synteny, and comparison of gene-family diversity across
species. The availability of this robust platform provides unprecedented opportunities to
elucidate the evolutionary history of flowering plants.