Ensembl Genomes 2016: more genomes, more complexity

By Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, B. J. Bolt, D. Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller and 28 more. Nucleic Acids Res., 2015

511 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/845936f1db153c77285efe8124da6da1ab376c0a

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Citations in the corpus

Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “Expression Atlas continues to reannotate and re-analyse data sets with each new Ensembl (12) and Ensembl Genomes (13) release, therefore keeping all data sets up-to-date with the latest genome annotations.”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “Other databases such as the DOE’s Joint Genome Institute Integrated Microbial Genomes & Microbiomes (JGI IMG/M) database (7), the PATRIC (Pathosystems Resource Integration Center) database (8) and Ensembl Bacteria (9) provide additional layers of information for the deposited genomes through integra”
RNAcentral: a hub of information for non-coding RNA sequences (2018, unknown): “We downloaded 296 genomes from Ensembl (6) and all Ensembl Genomes (7) divisions except Bacteria (due to scale).”
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017, background): “Since dedicated resources focusing on unicellular photosynthetic eukaryotes are available elsewhere (7,8), we decided to only incorporate a limited set of green algae to be used as outgroup for the new PLAZA 4.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, methodology): “It is compatible with any Ensembl infrastructure based resource including Ensembl Genomes (44), which has released its own installation of this service.”
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017, methodology): “3 4.6 Mb 382 130 Bacillus subtilis ASM904v1 4.2 Mb 250 53 Methanocaldococcus jannaschii ASM9166v1 1.7 Mb 276 18 Aquifex aeolicus ASM862v1 1.6 Mb 55 7 Borrelia burgdorferi ASM868v2 1.5 Mb 42 7 In future releases, we will supplement Rfamseq with genomes from Ensembl (1), Ensembl Genomes (12) and NCBI ”
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, methodology): “We retrieved bacterial and archaeal genomes from Ensembl Bacteria (26), and selected 3663 bacteria and 345 archaea for orthology analysis that have the most complete annotations, as estimated by the proxy of having the most of complete universal single-copy genes (27,28), and that best sample the ge”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “Its data feed into a host of annotation pipelines, including ENSEMBL (26), ENSEMBL Genomes (27), PDBe (28), BLAST2GO (29), PhytoPath (30), the digenic diseases database - DIDA (31), and the Endeavour candidate gene prioritisation server (32).”
Computational pan-genomics: status, promises and challenges (2016, methodology): “A sequence graph assembled from the Homo sapiens reference genome and all transcripts of the EEF1A1 gene in Ensembl v80 [93].”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, unknown): “The 2016 version of g:Profiler supports the analysis of data from 213 different organisms from Ensembl (19) and Ensembl Genomes (21).”