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.

Algal Genetics Group UMR 8227 CNRS Sorbonne Universite UPMC University Paris 06 Paris France

Andorra Research and Innovation Sant Julià de Lòria Andorra

Animal Breeding and Genomics Wageningen University and Research Wageningen The Netherlands

Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Bern Switzerland

Barcelona Supercomputing Center; Spanish National Bioinformatics Institute ELIXIR Spain Getafe Spain

Barcelona Supercomputing Centre Barcelona Spain

Berlin Center for Genomics in Biodiversity Research Berlin Germany

Biodiversity Research Center Academia Sinica Taipei Taiwan

Bioinformatics Group Department of Computer Science Albert Ludwigs University Freiburg Freiburg Germany

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairao Vairao Portugal

Catalan Institution for Research and Advanced Studies Barcelona Spain

CE3C Centre for Ecology Evolution and Environmental Changes and CHANGE Global Change and Sustainability Institute Faculdade de Ciências Universidade de Lisboa Campo Grande Lisboa Portugal

Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway

Centre for Palaeogenetics Stockholm Sweden

Centre of Applied Studies for the Sustainable Management and Protection of Mountain Areas CRC Ge S Di Mont University of Milan Milan Italy

Centro Nacional de Análisis Genómico Barcelona Spain

CIBER of Epidemiology and Public Health Granada Spain

CIBERINFEC Instituto Carlos 3 Barcelona Spain

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Pólo dos Açores; Faculdade de Ciências e Tecnologia Universidade dos Açores Ponta Delgada Portugal

CIBIO Centro de Investigacao em Biodiversidade e Recursos Geneticos InBIO Laboratorio Associado Universidade do Porto Vairao Portugal

CoNISMa Consorzio Nazionale Interuniversitario per le Scienze del Mare Roma Italy

Conservation Biology Research Group Department of Biology University of Malta Msida Malta

Departamento de Biologia Animal Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal

Departamento de Biología de la Conservación y Cambio Global Estación Biológica de Doñana CSIC Sevilla Spain

Departamento de Biologia Faculdade de Ciencias da Universidade do Porto Porto Portugal

Departamento de Biologia Faculdade de Ciencias Universidade do Porto Porto Portugal

Departamento de Biologia Vegetal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal

Department 4 Fish Biology Fisheries and Aquaculture Leibniz Institute of Freshwater Ecology and Inland Fisheries Berlin Germany

Department of Agricultural and Environmental Sciences Production Landscape Agroenergy University of Milan Milan Italy

Department of Agricultural and Environmental Sciences Production Landscape and Agroenergy DiSAA University of Milan Milan Italy

Department of Agricultural and Environmental Sciences University of Milan via Giovanni Celoria 2 Milan Italy

Department of Agricultural Sciences University of Naples Federico 2 Portici Italy

Department of Animal Ecology Netherlands Institute of Ecology Wageningen The Netherlands

Department of Biodiversity and Ecology Plant Science and Biodiversity Centre Slovak Academy of Sciences Bratislava Slovakia

Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales Madrid Spain

Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden

Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland

Department of Biological Geological and Environmental Sciences Alma Mater Studiorum Universitá di Bologna Bologna Italy

Department of Biology and Biotechnologies Sapienza University of Rome Rome Italy

Department of Biology and Biotechnology University of Pavia Pavia Italy

Department of Biology and Ecology University of Novi Sad Novi Sad Serbia

Department of Biology School of Sciences and Engineering University of Crete Voutes University Campus Irakleio Greece

Department of Biology University of Antwerp Antwerp Belgium

Department of Biology University of Florence Sesto Fiorentino Italy

Department of Biology University of Graz Graz Austria

Department of Biosciences Biotechnology and Environment University of Bari Aldo Moro Bari Italy

Department of Biosciences Università degli Studi di Milano Milan Italy

Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parma Italy

Department of Ecology and Evolution University of Lausanne Lausanne Switzerland

Department of Ecology and Genetics Uppsala University Uppsala Sweden

Department of Fish Ecology and Evolution Eawag Kastanienbaum Switzerland

Department of Genetics and Genomics Institute of Genetics and Biotechnology Hungarian University of Agriculture and Life Sciences Godollo Hungary

Department of Genetics University of Cambridge Cambridge UK

Department of Organismal Biology Universite libre de Bruxelles Brussels Belgium

Department of Zoology Faculty of Science Charles University Prague Czech Republic

Department of Zoology Faculty of Science Stockholm University Stockholm Sweden

Department of Zoology Hungarian Natural History Museum Budapest Hungary

Department of Zoology Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia

Department of Zoology Stockholm University Stockholm Sweden

Department of Zoology Swedish Museum of Natural History Stockholm Sweden

Digital Science London UK

Division of Evolutionary Ecology Institute of Ecology and Evolution University of Bern Bern Switzerland

Doctoral School of Biology Department of Systematic Zoology and Ecology Institute of Biology ELTE Eotvos Lorand University Budapest Hungary

DRESDEN concept Genome Center Dresden Germany

Eawag Swiss Federal Institute of Aquatic Science and Technology Department of Fish Ecology and Evolution Kastanienbaum Switzerland

Ecology and Genetics Research Unit University of Oulu Oulu Finland

Ecology Evolution and Conservation Biology Department of Biology KU Leuven Leuven Belgium

Egas Moniz Center for Interdisciplinary Research Egas Moniz School of Health and Science Caparica Portugal

ERISA Escola Superior de Saúde Ribeiro Sanches IPLUSO Lisboa Portugal

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK

Evolutionary Biology Program Department of Ecology and Genetics Uppsala University Uppsala Sweden

Faculdade de Psicologia Universidade de Lisboa Lisboa Portugal

Faculty of Biology University of Warsaw Warsaw Poland

Faculty of Environmental Protection Velenje Slovenia

Forest Ecology Unit Research and Innovation Centre Fondazione Edmund Mach San Michele All'Adige Italy

France Integrative Biology of Marine Models Station Biologique de Roscoff Roscoff France

Genomics Institute University of California Santa Cruz CA USA

Génomique Métabolique Genoscope Institut François Jacob CEA CNRS Univ Evry Université Paris Saclay Evry France

Genoscope Institut François Jacob CEA Université Paris Saclay Evry France

Groupe de Recherche et d Etude pour la Gestion de l Environnement Villandraut France

Hellenic Centre for Marine Research Heraklion Crete Greece

HUN REN ELTE MTM Integrative Ecology Research Group Budapest Hungary

InBios Conservation Genetics Laboratory University of Liege Liege Belgium

Institut Botànic de Barcelona IBB Passeig del Migdia s n Parc de Montjüic Barcelona Spain

Institut de Systematique Evolution Biodiversite Museum National d Histoire Naturelle CNRS Sorbonne Université EPHE Université des Antilles Paris France

Institute for Bioinformatics and Medical Informatics University of Tubingen Tubingen Germany

Institute for Medical Genetics and Applied Genomics University of Tubingen Tubingen Germany

Institute for Nuclear Research of the NAS of Ukraine Kyiv Ukraine

Institute for Research in Biomedicine Barcelona Spain

Institute for Sustainable Plant Protection National Research Council Sesto Fiorentino Italy

Institute of Biochemistry and Molecular Biology Faculty of Medicine University of Debrecen Debrecen Hungary

Institute of Biomembranes Bioenergetics and Molecular Biotechnologies Consiglio Nazionale delle Ricerche Bari Italy

Institute of Evolutionary Biology Barcelona Spain

Institute of Life and Environmental Sciences University of Iceland Reykjavik Iceland

Institute of Medical Genetics and Applied Genomics University of Tubingen Tubingen Germany

Institute of Microbiology of the Czech Academy of Sciences Praha Czech Republic

Institute of Zoology University of Cologne Cologne Germany

Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics University of Bern Bern Switzerland

Interuniversity Center for Studies on Bioinspired Agro Environmental Technology University of Naples Federico 2 Naples Italy

Laboratory of Biodiversity and Evolutionary Genomics KU Leuven Leuven Belgium

Laboratory of Food Systems Biotechnology Institute of Food Nutrition and Health ETH Zurich Zurich Switzerland

Leibniz Institut für Zoo und Wildtierforschung Berlin Germany

Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig Bonn Bonn Germany

Linking Landscape Environment Agriculture and Food Associated Laboratory TERRA Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal

LOEWE Centre for Translational Biodiversity Genomics Frankfurt Germany

MARE Marine and Environmental Sciences Centre ARNET Aquatic Research Network Lisboa Portugal

Marine and Environmental Sciences Centre Aquatic Research Network Instituto Universitário de Ciências Psicológicas Sociais e da Vida Lisboa Portugal

Marine Animal Ecology Group Wageningen University and Research Wageningen The Netherlands

Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany

MHNC UP Natural History and Science Museum of the University of Porto Porto Portugal

MME BirdLife Hungary Budapest Hungary

Museu Nacional de História Natural e da Ciência Lisboa Portugal

Museum and Institute of Zoology Polish Academy of Sciences Warsaw Poland

National Biodiversity Future Center Palermo Italy

National Bioinformatics Infrastructure Sweden Uppsala Sweden

Natural History Museum of Crete School of Sciences and Engineering University of Crete Irakleio Greece

Natural History Museum University of Oslo Blindern Oslo Norway

Naturalis Biodiversity Center Leiden The Netherlands

Nature Research Centre Debrecen Hungary

Nature Research Centre Vilnius Lithuania

Naturhistorisches Museum Bern Bern Switzerland

Neuromics Support Facility Department of Biomedical Sciences University of Antwerp Antwerp Belgium

Neuromics Support Facility VIB Center for Molecular Neurology VIB Antwerp Belgium

Next Generation Sequencing Platform University of Bern Bern Switzerland

NGS Competence Center Tubingen Tubingen Germany

NGS Competence Center Tubingen University of Tubingen Tubingen Germany

NNF Center for Biosustainability Technical University of Denmark Kongens Lyngby Denmark

Portugal Centre for Ecology Evolution and Environmental Changes Lisbon Portugal

Ruder Boskovic Institute Zagreb Croatia

School of Biology and Environmental Science University College Dublin Belfield Ireland

Science and Research Centre Koper Koper Slovenia

Science for Life Laboratory Department of Biochemistry and Biophysics Stockholm University Solna Sweden

SciLifeLab Solna Sweden

Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark

Senckenberg Research Institute Frankfurt Germany

Slovenian Museum of Natural History Ljubljana Slovenia

Sociedade Portuguesa de Botânica Lisbon Portugal

Sorbonne Université CNRS Biologie Intégrative des Organismes Marins Banyuls sur Mer France

Swiss Institute of Bioinformatics Lausanne Switzerland

The Earlham Institute Norwich Research Park Norwich UK

The Vertebrate Genome Laboratory The Rockefeller University New York NY USA

Tree of Life Wellcome Sanger Institute Hinxton Cambridge UK

UCD Conway Institute University College Dublin Belfield Ireland

UNESCO Chair Land Within Sea Biodiversity and Sustainability in Atlantic Islands Portugal

Universidade dos Acores Departamento de Biologia Ponta Delgada Portugal

Universitat de Barcelona Barcelona Spain

Universite Paris Saclay INRAE URGI Versailles France

University of Bari Aldo Moro Department of Biosciences Biotechnology and Environment; Institute of Biomembranes Bioenergetics and Molecular Biotechnologies Consiglio Nazionale delle Ricerche Bari Italy

University of Cologne Cologne Germany

University of Debrecen Centre for Agricultural Genomics and Biotechnology Debrecen Hungary

University of Eastern Finland Kuopio Finland

University of Ljubljana Biotechnical Faculty Department of Biology Ljubljana Slovenia

University of Maribor Faculty of Natural Sciences and Mathematics Maribor Slovenia

University of Namur Department of Biology URBE ILEE Namur Belgium

University of New Brunswick Saint John Saint John New Brunswick Canada

University of Primorska Faculty of Mathematics Natural Sciences and Information Technologies Koper Slovenia

University of the Azores cE3c Centre for Ecology Evolution and Environmental Changes Azorean Biodiversity Group CHANGE Global Change and Sustainability Institute Rua Capitão João d´Ávila Pico da Urze Angra do Heroísmo Portugal

Uppsala University Uppsala Sweden

VU University Amsterdam Amsterdam The Netherlands

Wageningen University and Research Wageningen The Netherlands

Wellcome CRUK Gurdon Institute University of Cambridge Cambridge UK

Wellcome Sanger Institute Cambridge UK

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