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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 #395802

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Author
item YATES, ANDREW - EMBL-EBI
item ALLEN, JAMES - EMBL-EBI
item AMODE, RIDWAN - EMBL-EBI
item AZOV, ANDREY - EMBL-EBI
item BARBA, MATHTHIEU - EMBL-EBI
item BECERRA, ANDRES - EMBL-EBI
item BHAI, JYOTHISH - EMBL-EBI
item CAMPBELL, LAHCEN - EMBL-EBI
item CARBAJO MANUEL, MARTINEZ - EMBL-EBI
item CHAKIACHVILI, MARC - EMBL-EBI
item CHOUGULE, KAPEEL - COLD SPRING HARBOR LABORATORY
item CHRISTENSEN, MIKKEL - EMBL-EBI
item CONTRERAS-MOREIRA, BRUNO - EMBL-EBI
item CUZICK, ALAYNE - ROTHAMSTED RESEARCH
item FIORETTO, LUCA DA RIN - EMBL-EBI
item DAVIS, PAUL - EMBL-EBI
item DE SILVA, NISHADI - EMBL-EBI
item DIAMANTAKIS, STAVROS - EMBL-EBI
item DYER, SARAH - EMBL-EBI
item ELSTER, JUSTIN - OREGON STATE UNIVERSITY
item FILIPPI, CARLA - EMBL-EBI
item GALL, ASTRID - EMBL-EBI
item GRIGORIADIS, DIONYSIOS - EMBL-EBI
item GUIJARRO-CLARKE, CRISTINA - EMBL-EBI
item GUPTA, PARUL - OREGON STATE UNIVERSITY
item HAMMOND-KOSACK, KIM - ROTHAMSTED RESEARCH
item HOWE, KEVIN - EMBL-EBI
item JAISWAL, PANKAJ - EMBL-EBI
item KAIKALA, VINAY - EMBL-EBI
item KUMAR, VIVEK - COLD SPRING HARBOR LABORATORY
item KUMARI, SUNITA - COLD SPRING HARBOR LABORATORY
item LANGRIDGE, NICK - EMBL-EBI
item LE, TUAN - EMBL-EBI
item LUYPAERT, MANUEL - EMBL-EBI
item MASLEN, GARETH - EMBL-EBI
item MAUREL, THOMAS - EMBL-EBI
item MOORE, BENJAMIN - EMBL-EBI
item MUFFATO, MATTHIEU - EMBL-EBI
item MUSHTAQ, ALEENA - EMBL-EBI
item NAAMATI, GUY - EMBL-EBI
item NAITHANI, SUSHMA - OREGON STATE UNIVERSITY
item OLSON, ANDREW - COLD SPRING HARBOR LABORATORY
item PARKER, ANNE - EMBL-EBI
item PAULINI, MICHAEL - EMBL-EBI
item PEDRO, HELDER - EMBL-EBI
item PERRY, EMILY - EMBL-EBI
item PREECE, JUSTIN - INSTITUTO DE CLIMA Y AGUA (INTA)
item QUINTON-TULLOCH, MARK - EMBL-EBI
item RODGERS, FAYE - WELLCOME TRUST SANGER INSTITUTE
item ROSELLO, MARC - EMBL-EBI
item RUFFIER, MAGALI - EMBL-EBI
item SEAGER, JAMES - ROTHAMSTED RESEARCH
item SITNIK, VASILY - EMBL-EBI
item SZPAK, MICHAL - EMBL-EBI
item TATE, JOHN - EMBL-EBI
item TELLO-RUIZ, MARCELA - COLD SPRING HARBOR LABORATORY
item TREVANION, STEPHEN - EMBL-EBI
item URBAN, MARTIN - ROTHAMSTED RESEARCH
item Ware, Doreen
item WEI, SHARON - COLD SPRING HARBOR LABORATORY
item WILLIAMS, GARY - EMBL-EBI
item WINTERBOTTOM, ANDREA - EMBL-EBI
item ZAROWIECKI, MAGDALENA - EMBL-EBI
item FINN, ROBERT - EMBL-EBI
item FLICEK, PAUL - EMBL-EBI

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/10/2021
Publication Date: 11/13/2021
Citation: Yates, A.D., Allen, J., Amode, R.M., Azov, A.G., Barba, M., Becerra, A., Bhai, J., Campbell, L.I., Carbajo Manuel, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Fioretto, L., Davis, P., De Silva, N.H., Diamantakis, S., Dyer, S., Elster, J., Filippi, C.V., Gall, A., Grigoriadis, D., Guijarro-Clarke, C., Gupta, P., Hammond-Kosack, K.E., Howe, K.L., Jaiswal, P., Kaikala, V., Kumar, V., Kumari, S., Langridge, N., Le, T., Luypaert, M., Maslen, G.L., Maurel, T., Moore, B., Muffato, M., Mushtaq, A., Naamati, G., Naithani, S., Olson, A., Parker, A., Paulini, M., Pedro, H., Perry, E., Preece, J., Quinton-Tulloch, M., Rodgers, F., Rosello, M., Ruffier, M., Seager, J., Sitnik, V., Szpak, M., Tate, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Ware, D., Wei, S., Williams, G., Winterbottom, A., Zarowiecki, M., Finn, R.D., Flicek, P. 2021. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. 50(D1):D996-D1003. https://doi.org/10.1093/nar/gkab1007.
DOI: https://doi.org/10.1093/nar/gkab1007

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 resource. Released together in a synchronized fashion, they provide genome sequence, annotation, variation, transcriptomic data and comparative analysis across the tree of life. In addition, Ensembl software tools and genome browser were created for consistent analysis, data mining and visualization to improve and deepen genome annotation and interpretation of the data for the scientific community. This article is an update of the recent developments and plans of Ensembl Genomes, reporting the largest increase in plant, metazoan and fungal genomes since its inception and its effort to reduce bacteria genome redundancy. Other advances include improvements on gene annotation and development of the Ensembl Rapid Release resource to speedup new genome releases, as well as the introduction of AlphaFold, a visualization tool for viewing predicted 3D protein structures in the AlphaFold Database (DB). Future effort will focus on improving support for the microbial research community and continued integration with Ensembl. AlphaFold has been a revolutionary advancement in 3D protein structure prediction, and the release of AlphaFold DB in July 2021 (Varadi et al - in preparation) made available predictions across 17 non-vertebrate species providing previously unimaginable 3D proteome coverage.

Technical Abstract: Ensembl Genomes (https://www.ensemblgenomes. org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl. org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle.