Ensembl Plants: An Integrating Resource for Plant Genomics and Variation

Ensembl Plants is an integrating portal for genome-scale data from plant genomes. Produced in collaboration with Gramene, Ensembl Plants includes data from important crop and model genomes, including Arabidopsis, rice, and maize. Recent additions include soybean and two evolutionary outliers, the spikemoss Selaginella and the green alga Chlamydomonas. Access to data is provided through a variety of interfaces including web browser, FTP, web services, Perl API, public SQL database and query-optimised data warehouse; the resource is updated 4-6 times each year. Integrated data include array probes, ESTs and protein alignments.; and protein and DNA-based comparative analysis, including pairwise and multiple sequence alignments. Additionally, we have developed variation databases for several species (including Arabidopsis, rice, grape and maize) incorporating data from the genome-wide array- and resequencing-based studies underway in many plants, providing information about the identification, distribution, functional and phenotypic consequences of SNPs and indels. The Arabidopsis variation database contains data from the 1001 genomes (and other) projects, and currently contains in excess of 14 million variations from over 1600 accessions. Ensembl Plants complements the coverage of animals in Ensembl, of plant pathogens in Ensembl Fungi and Ensembl Protists, and plant pests in Ensembl Metazoa, providing a common route of access to genomes of agricultural importance from across the taxonomic space.