P1132Grass Genomes in Ensembl Plants
Ensembl Plants (http://plants.ensembl.org) is an integrating portal for accessing data from plant species, providing access to data including genome sequence, gene annotation, polymorphism, and regulatory elements. The database currently contains data from 19 true grasses (Poaceae), including the hexaploid genome of bread wheat, which are in varying states of completion, from the well-assembled rice genome to the more fragmentary genomes of barley and wheat. Comparative analysis has identified conserved families and implied their evolutionary history, putting 600,980 Poaceae genes into 38,104 clusters, 7203 of which (containing 260,004 genes) are found in all Poaceae and 954 of which show a 1:1 relationship between all 21 genomes (counting the bread wheat A, B and D genomes separately). The orthologue calls are additionally supported by whole-genome alignments performed using lastZ, which are performed among many pairs of genomes including the different bread wheat genomes against each other. To facilitate browsing of bread wheat and other polyploid species, a new view has been developed showing the relationship between homoeologous regions, and separate tracks show polymorphisms and inter-homoeologue variations. Data is made publicly available through the browser, FTP, MySQL, Perl and REST-ful APIs and a query-optimised interface constructed with the data warehousing toolkit BioMart. Ensembl Plants is developed in close collaboration with Gramene database (http://www.gramene.org), and with our collaborators in the transPLANT project (http://transplantdb.eu).