Ensembl Genomes 2016: more genomes, more complexity

Paul Julian Kersey, James E Allen, Irina Armean, Sanjay Boddu, Bruce J Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Lee J Falin, Christoph Grabmueller, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K Aranganathan, Nicholas Langridge, Ernesto Lowy, Mark D McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee OngBert Overduin, Michael Paulini, Helder Pedro, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela Tello-Ruiz, Joshua Stein, Sharon Wei, Doreen Ware, Daniel M Bolser, Kevin L Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen, Daniel M Staines

Research output: Contribution to journalArticlepeer-review


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, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. 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.

Original languageEnglish
Pages (from-to)D574-D580
JournalNucleic Acids Research
Issue numberD1
Early online date17 Nov 2015
Publication statusPublished - 4 Jan 2016


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