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

Mc Cartney AM, Formenti G, Mouton A, De Panis D, Marins LS, Leitao HG, Diedericks G, Kirangwa J, Morselli M, Salces J, Escudero N, Iannucci A, Natali C, Svardal H, Fernandez R, De Pooter T, Joris G, Strazisar M, Wood J, Herron KE, Seehausen O, Watts PC, Shaw F, Davey RP, Minotto A, Fernandez Gonzalez JM, Bohne A, Alegria C, Alioto T, Alves PC, Amorim IR, Aury J-M, Backstrom N, Baldrian P, Ballarin L, Baltrunaite L, Barta E, BedHom B, Belser C, Bergsten J, Bertrand L, Bilandija H, Binzer-Panchal M, Bista I, Blaxter M, Borges PAV, Borges Dias G, Bosse M, Brown T, Bruggmann R, Buena-Atienza E, Burgin J, Buzan E, Cariani A, Casadei N, Chiara M, Chozas S, Ciampor F, Crottini A, Cruaud C, Cruz F, Dalen L, De Biase A, del Campo J, Delic T, Dennis AB, Derks MFL, Diroma MA, Djan M, Duprat S, Eleftheriadi K, Feulner PGD, Flot J-F, Forni G, Fosso B, Fournier P, Fournier-Chambrillon C, Gabaldon T, Garg S, Gissi C, Giupponi L, Gomez-Garrido J, Gonzalez J, Grilo ML, Gruening B, Guerin T, Guiglielmoni N, Gut M, Haesler MP, Hahn C, Halpern B, Harrison P, Heintz J, Hindrikson M, Hoglund J, Howe K, Hughes G, Istace B, Cock MJ, Jancekovic F, Jonsson ZO, Joye-Dind S, Koskimaki JJ, Krystufek B, Kubacka J, Kuhl H, Kusza S, Labadie K, Lahteenaro M, Lantz H, Lavrinienko A, Leclere L, Lopes RJ, Madsen O, Magdelenat G, Magoga G, Manousaki T, Mappes T, Marques JP, Martinez Redondo GI, Maumus F, McCarthy SA, Megens H-J, Melo-Ferreira J, Mendes SL, Montagna M, Moreno J, Mosbech M-B, Moura M, Musilova Z, Myers E, Nash WJ, Nater A, Nicholson P, Niell M, Nijland R, Noel B, Noren K, Oliveira PH, Olsen R-A, Ometto L, Oomen RA, Ossowski S, Palinauskas V, Palsson S, Panibe JP, Pauperio J, Pavlek M, Payen E, Pawlowska J, Pellicer J, Pesole G, Pimenta J, Pippel M, Pirttila AM, Poulakakis N, Rajan J, Rego RMC, Resendes R, Resl P, Riesgo A, Rodin-Morch P, Soares AER, Rodriguez Fernandes C, Romeiras MM, Roxo G, Ruber L, Ruiz-Lopez MJ, Saarma U, Silva LP, Sim-Sim M, Soler L, Sousa VC, Sousa Santos C, Spada A, Stefanovic M, Steger V, Stiller J, Stock M, Struck THH, Sudasinghe H, Tapanainen R, Tellgren-Roth C, Trindade H, Tukalenko Y, Urso I, Vacherie B, Van Belleghem SM, van Oers K, Vargas-Chavez C, Velickovic N, Vella N, Vella A, Vernesi C, Vicente S, Villa S, Vinnere Pettersson O, Volckaert FAM, Voros J, Wincker P, Winkler S, Ciofi C, Waterhouse RM, Mazzoni CJ. 2024. npj biodiversity 3, 28
DOI
10.1038/s44185-024-00054-6

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.