Ensembl Genomes: Genomic Resources for Plants, Pests, Pathogens and Pollinators

Ensembl Genomes (http://ensemblgenomes.org) is a resource for genome-scale data, covering bacteria, protists, fungi, plants and invertebrate metazoa, supplementing the coverage of vertebrate species by the Ensembl project (http://www.ensembl.org).  Collectively, Ensembl and Ensembl Genomes offer access to data from farm animals and crop plants, from pests, pathogens and pollinators and symbionts, via an interactive web browser and a variety of routes for programmatic access including Perl and RESTful APIs.  Data available include alignments, polymorphisms, comparative analysis, and functional annotation; in addition, tools are provided to allow users to perform sequence similarity search, coordinate projection and variant effect prediction.  Recent improvements include an extension of resource to handle the polyploid genome of bread wheat, and the up-scaling of pipelines to incorporate more fungal and protist genomes: the resource now contains over 500 eukaryotic microorganisms.  Two sister projects both using Ensembl technology cover plant pathogens: PhytoPath (http://phytopathdb.org) focuses on fungi and oomycetes, while WormBase ParaSite (http://parasite.wormbase.org) includes data from parasitic helminths.  A current focus of work is the automation of processes to represent RNA-seq data deposited in the ENA/GenBank/DDBJ archives as alignments on the reference genome, and of new tools to allow users to select such data for display.