Ensembl Genomes 2020-enabling non-vertebrate genomic research

Authors: HOWE, K. - European Bioinformatics Institute; CONTRERAS-MOREIRA, B. - European Bioinformatics Institute; DE SILVA, N. - European Bioinformatics Institute; MASLEN, G. - European Bioinformatics Institute; AKANNI, W. - European Bioinformatics Institute; ALLEN, J. - European Bioinformatics Institute; ALVAREZ-JARRETA, J. - European Bioinformatics Institute; BARBA, M. - European Bioinformatics Institute; BOLSER, D. - European Bioinformatics Institute; CAMBELL, L. - European Bioinformatics Institute; CARBAJO, M. - European Bioinformatics Institute; CHAKIACHVILI, M. - European Bioinformatics Institute; CHRISTENSEN, M. - European Bioinformatics Institute; CUMMINS, C. - European Bioinformatics Institute; CUZICK, A. - Rothamsted Research; DAVIS, P. - European Bioinformatics Institute; FEXOVA, S. - European Bioinformatics Institute; GALL, A. - European Bioinformatics Institute; GEORGE, N. - European Bioinformatics Institute; GIL, L. - European Bioinformatics Institute; GUPTA, P. - Oregon State University; HAMMOND-KOSACK, K. - Rothamsted Research; HASKELL, E. - European Bioinformatics Institute; HUNT, S. - European Bioinformatics Institute; JAISWAL, P. - Oregon State University; JANACEK, S. - European Bioinformatics Institute; KERSEY, P. - European Bioinformatics Institute; LANGRIDGE, N. - European Bioinformatics Institute; MAHESWARI, U. - European Bioinformatics Institute; MAUREL, T. - European Bioinformatics Institute; MCDOWALL, M. - European Bioinformatics Institute; MOORE, B. - European Bioinformatics Institute; MUFFATO, M. - European Bioinformatics Institute; NAAMATI, G. - European Bioinformatics Institute; NAITHANI, S. - Oregon State University; OLSON, A. - Cold Spring Harbor Laboratory; PAPATHEODOROU, I. - European Bioinformatics Institute; PATRICIO, M. - European Bioinformatics Institute; PAULINI, M. - European Bioinformatics Institute; PEDRO, H. - European Bioinformatics Institute; PERRY, E. - European Bioinformatics Institute; PREECE, J. - Oregon State University; ROSELLO, M. - European Bioinformatics Institute; RUSSELL, M. - European Bioinformatics Institute; SITNIK, V. - European Bioinformatics Institute; STAINES, D. - European Bioinformatics Institute; STEIN, J. - Cold Spring Harbor Laboratory; TELLO-RUIZ, M. - Cold Spring Harbor Laboratory; TREVANION, S. - European Bioinformatics Institute; URBAN, M. - Rothamsted Research; WEI, S. - Cold Spring Harbor Laboratory; Ware, Doreen; WILLIAMS, G. - European Bioinformatics Institute; YATES, A. - European Bioinformatics Institute; FLICEK, P. - European Bioinformatics Institute

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2019
Publication Date: 1/8/2020
Citation: Howe, K.L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D.M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., Gil, L., Gupta, P., Hammond-Kosack, K.E., Haskell, E., Hunt, S.E., Jaiswal, P., Janacek, S.H., Kersey, P.J., Langridge, N., Maheswari, U., Maurel, T., Mcdowall, M.D., Moore, B., Muffato, M., Naamati, G., Naithani, S., Olson, A., Papatheodorou, I., Patricio, M., Paulini, M., Pedro, H., Perry, E., Preece, J., Rosello, M., Russell, M., Sitnik, V., Staines, D.M., Stein, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Wei, S., Ware, D., Williams, G., Yates, A.D., Flicek, P. 2020. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Research. 48(D1,8):D689-D695. https://doi.org/10.1093/nar/gkz890.
DOI: https://doi.org/10.1093/nar/gkz890

Interpretive Summary: Ensembl Genomes is an online resource that integrates genome-scale data for five groups: plants, bacteria, protists, fungi and invertebrate metazoa. The Ensembl Genomes group harnessed the integrative power of Ensembl tools for comparative analysis, data mining and visualization across genomes of scientific interest, working in collaboration with scientific communities to improve genome annotation and interpretation. This article reports an update of 22 new plant genome assemblies; gene expression data for 12 plant species including rice, maize, sorghum, barley, tomato, and wheat; and 50 new manually curated pathways, in collaboration with the Gramene and EBI Gene Expression Atlas projects. Two central figures in the article display how the expression and pathways data are made available through embedded computational widgets. Specifically for gene expression, the widget consists of interactive anatomical diagrams of plant and seed that indicate where a protein is expressed according to distinct published studies.

Technical Abstract: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genomescale 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 interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.