Ensembl genomes 2016: more genomes, more complexity

Authors: KERSEY, PAUL - European Bioinformatics Institute; ALLEN, JAMES - European Bioinformatics Institute; ARMEAN, IRINA - European Bioinformatics Institute; BODDU, SANJAY - European Bioinformatics Institute; BOLT, BRUCE - European Bioinformatics Institute; CARVALHO-SILVA, DENISE - European Bioinformatics Institute; CHRISTENSEN, MIKKEL - European Bioinformatics Institute; DAVIS, PAUL - European Bioinformatics Institute; FALIN, LEE - European Bioinformatics Institute; GRABMUELLER, CHRISTOPH - European Bioinformatics Institute; HUMPHREY, JAY - European Bioinformatics Institute; KERHORNOU, ARNAUD - European Bioinformatics Institute; KHOBOVA, JULIA - European Bioinformatics Institute; ARANGANATHAN, NAVEEN - European Bioinformatics Institute; LANGRIDGE, NICHOLAS - European Bioinformatics Institute; LOWY, ERNESTO - European Bioinformatics Institute; MCDOWALL, MARK - European Bioinformatics Institute; MAHESWARI, UMA - European Bioinformatics Institute; NUHN, MICHAEL - European Bioinformatics Institute; ONG, CHUANG KEE - European Bioinformatics Institute; OVERDUIN, BERT - European Bioinformatics Institute; PAULINI, MICHAEL - European Bioinformatics Institute; PEDRO, HELDER - European Bioinformatics Institute; PERRY, EMILY - European Bioinformatics Institute; SPUDICH, GIULLETTA - European Bioinformatics Institute; TAPANARI, ELECTRA - European Bioinformatics Institute; WALTS, BRANDON - European Bioinformatics Institute; WILLIAMS, GARETH - European Bioinformatics Institute; MARCELA-TELLO, MARCELA - European Bioinformatics Institute; STEIN, JOSHUA - Cold Spring Harbor Laboratory; WEI, SHARON - Cold Spring Harbor Laboratory; Ware, Doreen; BOISER, DANIEL - European Bioinformatics Institute; HOWE, KEVIN - European Bioinformatics Institute; KULESHA, EUGENE - European Bioinformatics Institute; LAWSON, DANIEL - European Bioinformatics Institute; MASLEN, GARETH - European Bioinformatics Institute; STAINES, DANIEL - European Bioinformatics Institute

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2015
Publication Date: 1/4/2016
Publication URL: http://DOI: 10.1093/nar/gkv 1209
Citation: Kersey, P.J., Allen, J., Armean, I., Boddu, S., Bolt, B.J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C., Humphrey, J., Kerhornou, A., Khobova, J., Aranganathan, N.K., Langridge, N., Lowy, E., Mcdowall, M.D., Maheswari, U., Nuhn, M., Ong, C., Overduin, B., Paulini, M., Pedro, H., Perry, E., Spudich, G., Tapanari, E., Walts, B., Williams, G., Marcela-Tello, M., Stein, J., Wei, S., Ware, D., Boiser, D.M., Howe, K.L., Kulesha, E., Lawson, D., Maslen, G., Staines, D.M. 2016. Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Research. 44:D574-D580.

Interpretive Summary: Ensembl Genomes is an online resource that integrates genome-scale data for five non-vertebrate groups: plants, bacteria, protists, fungi and invertebrate metazoan. It complements the Ensembl genome annotation system created in 2000 for the annotation, analysis and display of vertebrate genomes; thus enabling users to use a single collection of (interactive and programmatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In this update, the team highlighted the development of new analyses and views to represent polyploid genomes like the bread wheat, their data expansion, and current efforts to automate integration of archival genome data including associated RNA sequence and genetic variant calls.

Technical Abstract: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23,000 bacterial genomes, 400 fungal genomes and 100 protist genomes. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.