The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

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Publication Details

Journal
npj Biodiversity
Published
2024-09-17
DOI
https://doi.org/10.1038/s44185-024-00054-6
Citations
41
Primary Topic
Genomics and Phylogenetic Studies
Type
article
Field-Weighted Citation Impact
9.35

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article

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Zophonı́as O. Jónsson, Judit Vörös, Christoph Hahn, José Melo‐Ferreira et al.
41 citations
npj Biodiversity
Genomics and Phylogenetic Studies
9.35
article

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Zophonı́as O. Jónsson, Judit Vörös, Christoph Hahn, José Melo‐Ferreira, Felix Shaw, Marcel P. Haesler, Graham M. Hughes, Matteo Montagna, Nevena Veličković, Graziano Pesole, Isabel Rosário Amorim, Janne J. Koskimäki, Pascal Fournier, Claúdio Ciofi, Henrik Lantz, Hiranya Sudasinghe, Björn Grüning, Jonathan M. D. Wood, Benjamin Noël, Zuzana Musilová, Joseph Kirangwa, Lucile Solér, Karin Norén, Gemma I. Martínez‐Redondo, Patrick Wincker, Ann M. Mc Cartney, Karine Labadie, Niclas Backström, Johannes Bergsten, Ana Riesgo, Tyler Alioto, Mirte Bosse, Vítor C. Sousa, Urmas Saarma, Szilvia Kusza, Philipp Resl, Tereza Manousaki, João Pimenta, Kees van Oers, Adriana Vella, Julia Heintz, Carla Sousa‐Santos, Giulio Formenti, Mojca Stražišar, Mihajla Djan, Ricardo J. Lopes, Teo Delić, Reindert Nijland, Sara Vicente, Guilherme Borges Dias, Meri Lähteenaro, Cristiano Vernesi, Heiner Kuhl, Noel Vella, Elena Buena‐Atienza, Justyna Kubacka, Bertrand Bed’Hom, João Pedro Marques, Alice Minotto, Rúben M. Correia Rego, Tapio Mappes, Jaume Pellicer, Eugene Tukalenko, Alessia Cariani, Robert Davey, Roberto Resendes, Nadège Guiglielmoni, Bálint Halpern, Klara Eleftheriadi, Caroline Belser, Snæbjörn Pálsson, Will Nash, Judit Salces-Ortiz, Shane McCarthy, Astrid Böhne, Maria Manuel Romeiras, Patrik Rödin‐Mörch, Josefin Stiller, Marco Morselli, Anna Maria Pirttilä, Genevieve Diedericks, Rebekah A. Oomen, Hendrik‐Jan Megens, Matthias Stöck, Fedor Čiampor, Iliana Bista, Julia Pawłowska, Love Dalén, Tom Brown, María José Ruiz‐López, Petr Baldrián, Martijn F. L. Derks, Tim De Pooter, Carmela Gissi, Philine G. D. Feulner, Geert Joris, ‎Jacob Höglund, Elena Bužan, Miguel L. Grilo, Alessio Iannucci, Lukas Rüber, Kerstin Howe, Nicolas Casadei, Nikos Poulakakis, Phillip C. Watts, Benjamin Istace, Filip Volckaert, Corinne Cruaud, Ole Seehausen C D, Endre Barta, Carlos Fernandes, Martina Pavlek, Joana Paupério, Milomir Stefanović, Lucas Leclère, Sofia L. Mendes, Hannes Svardal, Peter W. Harrison, Josephine Burgin, Nuria Escudero, Angelica Crottini, Benoît Vacherie, Shilpa Garg, Mark Blaxter, Christian Tellgren‐Roth, Javier del Campo, Laima Baltrūnaitė, Paulo A. V. Borges, Mónica Moura, Ilenia Urso, Chiara Natali, Giulia Magoga, Simone Duprat, Bruno Fosso, Boris Kryštufek, Maris Hindrikson, Robert Michael Waterhouse, Eugene Wimberly Myers, Jeremy Mark Cock, Jean‐Marc Aury, Guilherme Roxo, Anton Lavrinienko, Sérgio Chozas, Manuela Sim‐Sim, Camila J. Mazzoni, Lino Ometto, Carla Alegria, Jerome P. Panibe, Rosa Fernández, Fernando Cruz, Helena Trindade, André E. R. Soares, Henrique G. Leitão, José M. Fernández, Luca Giupponi, Olga Vinnere Pettersson, Laurie Bertrand, Alice B. Dennis, Sylke Winkler, Alice Mouton, Vaidas Palinauskas, Christine Fournier‐Chambrillon, Carlos Vargas-Chávez, Jeena Rajan, Paulo C. Alves, Pedro H. Oliveira, Matteo Chiara, Rémy Bruggmann, Franc Janžekovič, Martin Pippel, Pamela Nicholson, Alexander Nater, Mahesh Panchal, Florian Maumus, Sara Villa, Stephan Ossowski, Alberto Spada, Alessio De Biase, Jèssica Gómez‐Garrido, Maria Angela Diroma, Steven M. Van Belleghem, Josefa González, Giobbe Forni, Luís P. da Silva, Jean‐François Flot, Torsten H. Struck, Sagane Joye-Dind, Katie E Herron, Ole Madsen, Viktor Stéger, Marta Ortova Gut, Thomas Guérin, Emilie Payen, Remi‐André Olsen, Riikka Tapanainen, Helena Bilandija, Mai‐Britt Mosbech, Luísa S. Marins, Ghislaine Magdelenat, Toni Gabaldon, Diego De Panis, Manuel Niell, Joao Moreno
article en
41 citations

Abstract

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

npj BiodiversityVol. 3(1)
University College Dublin (IE), Fondazione Edmund Mach (IT), Eötvös Loránd University (HU), University of New Brunswick (CA), École Normale Supérieure Paris-Saclay (FR), Universidade dos Açores (PT), University of Bern (CH), University of Primorska (SI), Institució Catalana de Recerca i Estudis Avançats (ES), Uppsala University (SE), University of Copenhagen (DK), University of Parma (IT), SIB Swiss Institute of Bioinformatics (CH), Magyar Agrár- és Élettudományi Egyetem (HU), Centre National de la Recherche Scientifique (FR), Naturalis Biodiversity Center (NL), European Bioinformatics Institute (GB), Université Libre de Bruxelles (BE), University of Debrecen (HU), Gregor Mendel Institute of Molecular Plant Biology (AT), Austrian Academy of Sciences (AT), University of Lisbon (PT), University of Crete (GR), University of Antwerp (BE), University of Namur (BE), University of Ljubljana (SI), University of Graz (AT), University of Liège (BE), École Pratique des Hautes Études (FR), University of Freiburg (DE), Stockholm University (SE), University of Iceland (IS), Universitat Pompeu Fabra (ES), University of Novi Sad (RS), University of Eastern Finland (FI), Northern Michigan University (US), University of Cologne (DE), Universidade do Porto (PT), University of Oslo (NO), University of California, Santa Cruz (US), University of Milan (IT), University of Malta (MT), Czech Academy of Sciences (CZ), Université Paris Cité (FR), Slovak Academy of Sciences (SK), Charles University (CZ), University of Cambridge (GB), University of Pavia (IT), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), Université Paris-Saclay (FR), Norwich Research Park (GB), Slovenian Museum of Natural History (SI), Barcelona Supercomputing Center (ES), Hungarian Natural History Museum (HU), Science for Life Laboratory (SE), Instituto de Salud Carlos III (ES), Swedish Museum of Natural History (SE), The Gurdon Institute (GB), Station Biologique de Roscoff (FR), Wellcome Sanger Institute (GB), Senckenberg Research Institute and Natural History Museum Frankfurt/M (DE), Museum and Institute of Zoology (PL), Escola Superior de Saúde Egas Moniz (PT), Instituto Superior de Gestão (PT), ETH Zurich (CH), University of Maribor (SI), Sorbonne Université (FR), Laboratoire de Biologie Intégrative des Modèles Marins (FR), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Institute for Sustainable Plant Protection (IT), Estación Biológica de Doñana (ES), Natural History Museum of Bern (CH), Atlântica Instituto Universitário (PT), Sustainability Institute (ZA), Institute of Botany of the Slovak Academy of Sciences (SK), Institut Botànic de Barcelona (ES), University of Andorra (AD), CoNISMa (IT), Zoological Research Museum Alexander Koenig (DE), Earlham Institute (GB), ISPA - Instituto Universitário (PT), Institute of Biochemistry (HU), Institut de Systématique, Évolution, Biodiversité (FR), Sociedade Portuguesa de Cardiologia (PT), Netherlands Institute of Ecology (NL), Genoscope (FR), Leibniz Institute of Freshwater Ecology and Inland Fisheries (DE), Federico II University Hospital (IT), Berlin Center for Genomics in Biodiversity Research (DE), Digital Science (United Kingdom) (GB), Museo Nacional de Ciencias Naturales (ES), College of Environmental Protection (SI), Institute for Research in Biomedicine (ES), LOEWE Centre for Translational Biodiversity Genomics (DE), Czech Academy of Sciences, Institute of Microbiology (CZ), Ruđer Bošković Institute (HR), CEA Paris-Saclay (FR), Biologie Intégrative des Organismes Marins (FR), Hellenic Centre for Marine Research (GR), VIB-UAntwerp Center for Molecular Neurology (BE), Centre for Research in Anthropology (PT), Nature Research Centre (LT), Bernstein Center for Computational Neuroscience Tübingen (DE), Institut de Biologia Evolutiva (ES), Laboratoire de Biométrie et Biologie Evolutive (FR), Centre for Genomic Regulation (ES), Biodiversity Research Center, Academia Sinica (TW), VIB-VUB Center for Structural Biology (BE), Magyar Madártani és Természetvédelmi Egyesület (HU), Centro Nacional de Análisis Genómico (ES), Vienna Biocenter (AT), Institute for Nuclear Research (UA), Escola Superior de Saúde Ribeiro Sanches (PT), Centro Interuniversitário de História das Ciências e da Tecnologia (PT), Center for Systems Biology Dresden (DE), Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IT), Centre for Palaeogenetics (SE), Leibniz Institute for Zoo and Wildlife Research (DE), Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (ES), National Research Council (IT), Institute of Genetics (HU), Instituto de Estructura de la Materia (ES), Max Planck Institute of Molecular Cell Biology and Genetics (DE), National Bioinformatics Infrastructure Sweden, Leibniz Institute for the Analysis of Biodiversity Change (DE), Andorra Recerca + Innovació, Museu Nacional de História Natural e da Ciência, University of Florence (IT), University of Warsaw (PL), University of Bari Aldo Moro (IT), University of Tartu (EE), Swiss Federal Institute of Aquatic Science and Technology (CH), University of Montana (US), University of Naples Federico II (IT), Universitat de Barcelona (ES), Instituut voor Tropische Geneeskunde (BE), University of Tübingen (DE), Rockefeller University (US), Sapienza University of Rome (IT), Wellcome Trust (GB), Wageningen University & Research (NL), University of Bologna (IT), University of Jyväskylä (FI), Universitat Politècnica de Catalunya (ES), Technical University of Denmark (DK), University of Lausanne (CH), University of Oulu (FI), KU Leuven (BE), Polish Academy of Sciences (PL)
Helsingin Yliopisto, Université du Luxembourg, Oxford Brookes University, Università degli Studi di Milano, Direction Régionale de l'Environnement, de l'Aménagement et du Logement PACA, Tel Aviv University, Universidade de Lisboa, Université de Bordeaux, Université de Lausanne, Uniwersytet Warszawski, Uppsala Universitet, Institut Ruđer Bošković, Office Français de la Biodiversité, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biotechnology and Biological Sciences Research Council, Fundação para a Ciência e a Tecnologia
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