Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #326566

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: Ensembl genomes 2016: more genomes, more complexity

Author
item Kersey, Paul - European Bioinformatics Institute
item Allen, James - European Bioinformatics Institute
item Armean, Irina - European Bioinformatics Institute
item Boddu, Sanjay - European Bioinformatics Institute
item Bolt, Bruce - European Bioinformatics Institute
item Carvalho-silva, Denise - European Bioinformatics Institute
item Christensen, Mikkel - European Bioinformatics Institute
item Davis, Paul - European Bioinformatics Institute
item Falin, Lee - European Bioinformatics Institute
item Grabmueller, Christoph - European Bioinformatics Institute
item Humphrey, Jay - European Bioinformatics Institute
item Kerhornou, Arnaud - European Bioinformatics Institute
item Khobova, Julia - European Bioinformatics Institute
item Aranganathan, Naveen - European Bioinformatics Institute
item Langridge, Nicholas - European Bioinformatics Institute
item Lowy, Ernesto - European Bioinformatics Institute
item Mcdowall, Mark - European Bioinformatics Institute
item Maheswari, Uma - European Bioinformatics Institute
item Nuhn, Michael - European Bioinformatics Institute
item Ong, Chuang Kee - European Bioinformatics Institute
item Overduin, Bert - European Bioinformatics Institute
item Paulini, Michael - European Bioinformatics Institute
item Pedro, Helder - European Bioinformatics Institute
item Perry, Emily - European Bioinformatics Institute
item Spudich, Giulletta - European Bioinformatics Institute
item Tapanari, Electra - European Bioinformatics Institute
item Walts, Brandon - European Bioinformatics Institute
item Williams, Gareth - European Bioinformatics Institute
item Marcela-tello, Marcela - European Bioinformatics Institute
item Stein, Joshua - Cold Spring Harbor Laboratory
item Wei, Sharon - Cold Spring Harbor Laboratory
item Ware, Doreen
item Boiser, Daniel - European Bioinformatics Institute
item Howe, Kevin - European Bioinformatics Institute
item Kulesha, Eugene - European Bioinformatics Institute
item Lawson, Daniel - European Bioinformatics Institute
item Maslen, Gareth - European Bioinformatics Institute
item 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.