npj Biodiversity (Sep 2024)

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

  • Ann M. Mc Cartney,
  • Giulio Formenti,
  • Alice Mouton,
  • Diego De Panis,
  • Luísa S. Marins,
  • Henrique G. Leitão,
  • Genevieve Diedericks,
  • Joseph Kirangwa,
  • Marco Morselli,
  • Judit Salces-Ortiz,
  • Nuria Escudero,
  • Alessio Iannucci,
  • Chiara Natali,
  • Hannes Svardal,
  • Rosa Fernández,
  • Tim De Pooter,
  • Geert Joris,
  • Mojca Strazisar,
  • Jonathan M. D. Wood,
  • Katie E. Herron,
  • Ole Seehausen,
  • Phillip C. Watts,
  • Felix Shaw,
  • Robert P. Davey,
  • Alice Minotto,
  • José M. Fernández,
  • Astrid Böhne,
  • Carla Alegria,
  • Tyler Alioto,
  • Paulo C. Alves,
  • Isabel R. Amorim,
  • Jean-Marc Aury,
  • Niclas Backstrom,
  • Petr Baldrian,
  • Laima Baltrunaite,
  • Endre Barta,
  • Bertrand BedHom,
  • Caroline Belser,
  • Johannes Bergsten,
  • Laurie Bertrand,
  • Helena Bilandija,
  • Mahesh Binzer-Panchal,
  • Iliana Bista,
  • Mark Blaxter,
  • Paulo A. V. Borges,
  • Guilherme Borges Dias,
  • Mirte Bosse,
  • Tom Brown,
  • Rémy Bruggmann,
  • Elena Buena-Atienza,
  • Josephine Burgin,
  • Elena Buzan,
  • Alessia Cariani,
  • Nicolas Casadei,
  • Matteo Chiara,
  • Sergio Chozas,
  • Fedor Čiampor,
  • Angelica Crottini,
  • Corinne Cruaud,
  • Fernando Cruz,
  • Love Dalen,
  • Alessio De Biase,
  • Javier del Campo,
  • Teo Delic,
  • Alice B. Dennis,
  • Martijn F. L. Derks,
  • Maria Angela Diroma,
  • Mihajla Djan,
  • Simone Duprat,
  • Klara Eleftheriadi,
  • Philine G. D. Feulner,
  • Jean-François Flot,
  • Giobbe Forni,
  • Bruno Fosso,
  • Pascal Fournier,
  • Christine Fournier-Chambrillon,
  • Toni Gabaldon,
  • Shilpa Garg,
  • Carmela Gissi,
  • Luca Giupponi,
  • Jessica Gomez-Garrido,
  • Josefa González,
  • Miguel L. Grilo,
  • Björn Grüning,
  • Thomas Guerin,
  • Nadege Guiglielmoni,
  • Marta Gut,
  • Marcel P. Haesler,
  • Christoph Hahn,
  • Balint Halpern,
  • Peter W. Harrison,
  • Julia Heintz,
  • Maris Hindrikson,
  • Jacob Höglund,
  • Kerstin Howe,
  • Graham M. Hughes,
  • Benjamin Istace,
  • Mark J. Cock,
  • Franc Janžekovič,
  • Zophonias O. Jonsson,
  • Sagane Joye-Dind,
  • Janne J. Koskimäki,
  • Boris Krystufek,
  • Justyna Kubacka,
  • Heiner Kuhl,
  • Szilvia Kusza,
  • Karine Labadie,
  • Meri Lähteenaro,
  • Henrik Lantz,
  • Anton Lavrinienko,
  • Lucas Leclère,
  • Ricardo Jorge Lopes,
  • Ole Madsen,
  • Ghislaine Magdelenat,
  • Giulia Magoga,
  • Tereza Manousaki,
  • Tapio Mappes,
  • Joao Pedro Marques,
  • Gemma I. Martinez Redondo,
  • Florian Maumus,
  • Shane A. McCarthy,
  • Hendrik-Jan Megens,
  • Jose Melo-Ferreira,
  • Sofia L. Mendes,
  • Matteo Montagna,
  • Joao Moreno,
  • Mai-Britt Mosbech,
  • Mónica Moura,
  • Zuzana Musilova,
  • Eugene Myers,
  • Will J. Nash,
  • Alexander Nater,
  • Pamela Nicholson,
  • Manuel Niell,
  • Reindert Nijland,
  • Benjamin Noel,
  • Karin Noren,
  • Pedro H. Oliveira,
  • Remi-Andre Olsen,
  • Lino Ometto,
  • Rebekah A. Oomen,
  • Stephan Ossowski,
  • Vaidas Palinauskas,
  • Snaebjorn Palsson,
  • Jerome P. Panibe,
  • Joana Pauperio,
  • Martina Pavlek,
  • Emilie Payen,
  • Julia Pawlowska,
  • Jaume Pellicer,
  • Graziano Pesole,
  • Joao Pimenta,
  • Martin Pippel,
  • Anna Maria Pirttilä,
  • Nikos Poulakakis,
  • Jeena Rajan,
  • Rúben M.C. Rego,
  • Roberto Resendes,
  • Philipp Resl,
  • Ana Riesgo,
  • Patrik Rodin-Morch,
  • Andre E. R. Soares,
  • Carlos Rodriguez Fernandes,
  • Maria M. Romeiras,
  • Guilherme Roxo,
  • Lukas Rüber,
  • Maria Jose Ruiz-Lopez,
  • Urmas Saarma,
  • Luis P. da Silva,
  • Manuela Sim-Sim,
  • Lucile Soler,
  • Vitor C. Sousa,
  • Carla Sousa Santos,
  • Alberto Spada,
  • Milomir Stefanovic,
  • Viktor Steger,
  • Josefin Stiller,
  • Matthias Stöck,
  • Torsten H. Struck,
  • Hiranya Sudasinghe,
  • Riikka Tapanainen,
  • Christian Tellgren-Roth,
  • Helena Trindade,
  • Yevhen Tukalenko,
  • Ilenia Urso,
  • Benoit Vacherie,
  • Steven M. Van Belleghem,
  • Kees Van Oers,
  • Carlos Vargas-Chavez,
  • Nevena Velickovic,
  • Noel Vella,
  • Adriana Vella,
  • Cristiano Vernesi,
  • Sara Vicente,
  • Sara Villa,
  • Olga Vinnere Pettersson,
  • Filip A. M. Volckaert,
  • Judit Voros,
  • Patrick Wincker,
  • Sylke Winkler,
  • Claudio Ciofi,
  • Robert M. Waterhouse,
  • Camila J. Mazzoni

DOI
https://doi.org/10.1038/s44185-024-00054-6
Journal volume & issue
Vol. 3, no. 1
pp. 1 – 17

Abstract

Read online

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.