| Title: |
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics |
| Authors: |
Mc Cartney, Ann, M; Formenti, Giulio; Mouton, Alice; de Panis, Diego; Marins, Luísa, S; Leitão, Henrique, G; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco; Salces-Ortiz, Judit; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; de Pooter, Tim; Joris, Geert; Strazisar, Mojca; Wood, Jo; Herron, Katie, E; Seehausen, Ole; Watts, Phillip, C; Shaw, Felix; Davey, Robert, P; Minotto, Alice; Fernández, José, M; Böhne, Astrid; Alegria, Carla; Alioto, Tyler; Alves, Paulo, C; Amorim, Isabel, R; Aury, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; Bed’hom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandžija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo, Av; Borges Dias, Guilherme; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Casadei, Nicolas; Chiara, Matteo; Chozas, Sergio; Čiampor, Fedor; Crottini, Angelica; Cruaud, Corinne; Cruz, Fernando; Dalen, Love; de Biase, Alessio; del Campo, Javier; Delić, Teo; Dennis, Alice, B; Derks, Martijn, Fl; Diroma, Maria, Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine, Gd; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; Fournier-Chambrillon, Christine; Gabaldon, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gómez-Garrido, Jèssica; González, Josefa; Grilo, Miguel, L; Gruening, Bjoern; Guérin, Thomas; Guiglielmoni, Nadège; Gut, Marta; Haesler, Marcel, P; Hahn, Christoph; Halpern, Balint; Harrison, Peter; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham; Istace, Benjamin; Cock, Mark, J; Jancekovic, Franc; Jónsson, Zophonías, O; Joye-Dind, Sagane; Koskimaki, Janne, J; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lahteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclère, Lucas; Lopes, Ricardo, Jorge; Madsen, Ole; Magdelenat, Ghislaine; Magoga, Giulia; Manousaki, Tereza; Mappes, Tapio; Marques, João, P; Martinez Redondo, Gemma, I; Maumus, Florian; Megens, Hendrik-Jan; Melo-Ferreira, José; Mendes, Sofia, L; Montagna, Matteo; Moreno, João; Mosbech, Mai-Britt; Moura, Monica; Musilova, Zuzana; Myers, Eugene; Nash, Will, J; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Norén, Karin; Oliveira, Pedro H.; Olsen, Remi-Andre; Ometto, Lino; Ossowski, Stephan; Palinauskas, Vaidas; Pálsson, Snæbjörn; Panibe, Jerome, P; Paupério, Joana; Pavlek, Martina; Payen, Emilie; Pawłowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, Joao; Pippel, Martin; Pirttilä, Anna, Maria; Poulakakis, Nikos; Rajan, Jeena; Rego, Ruben, Mc; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rödin-Mörch, Patrik; Soares, André, Er; Rodríguez Fernandes, Carlos; Romeiras, Maria, M; Roxo, Guilherme; Ruber, Lukas; Ruiz-López, María, José; Saarma, Urmas; Silva, Luis, P; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor, C; Sousa Santos, Carla; Spada, Alberto; Stefanović, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten, Hugo H; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; van Belleghem, Steven, M; van Oers, Kees; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Vinnere Pettersson, Olga; Volckaert, Filip, Am; Vörös, Judit; Wincker, Patrick; Winkler, Sylke; Ciofi, Claudio; Waterhouse, Robert, M; Mazzoni, Camila, J |
| Contributors: |
Santa Cruz Genomics Institute; University of California Santa Cruz (UC Santa Cruz); University of California (UC)-University of California (UC); Institut de Systématique, Evolution, Biodiversité (ISYEB); Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA); Centre National de la Recherche Scientifique (CNRS); Station biologique de Roscoff = Roscoff Marine Station (SBR); Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS); Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M); Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff = Roscoff Marine Station (SBR); Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS); Station biologique de Roscoff Roscoff (SBR); Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS); Genoscope - Centre national de séquençage Evry (GENOSCOPE); Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)); Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA); Génomique métabolique (UMR 8030); Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)); Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS); Université Paris-Saclay; ANR-10-INBS-0009,France Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010); European Project: 101017207,H2020-INFRAEOSC-2018-2020,H2020-INFRAEOSC-2020-2,DICE(2021); European Project: 948281,ERC-2020-STG,ERC-2020-STG,SEA2LAND(2021); European Project: 676559,H2020-INFRADEV-2014-2015,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015); European Project: 101059492,HORIZON-CL6-2021-BIODIV-01,HORIZON-CL6-2021-BIODIV-01,BGE(2022); European Project: 724173,ERC-2016-COG,ERC-2016-COG,RETVOLUTION(2018); European Project: 324602,ERC-2012-PoC,ERC-2012-PoC,DD-PD(2012) |
| Source: |
https://hal.science/hal-04406124 ; 2024. |
| Publisher Information: |
CCSD |
| Publication Year: |
2024 |
| Subject Terms: |
[SDV]Life Sciences [q-bio] |
| Description: |
A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects. |
| Document Type: |
report |
| Language: |
English |
| Relation: |
info:eu-repo/grantAgreement//101017207/EU/Data Infrastructure Capacity for EOSC/DICE; info:eu-repo/grantAgreement//948281/EU/Land animal evolution: genomic landmarks on the path to terrestrial life/SEA2LAND; info:eu-repo/grantAgreement//676559/EU/ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences./ELIXIR-EXCELERATE; info:eu-repo/grantAgreement//101059492/EU/Biodiversity Genomics Europe/BGE; info:eu-repo/grantAgreement//724173/EU/Reticulate evolution: patterns and impacts of non-vertical inheritance in eukaryotic genomes./RETVOLUTION; info:eu-repo/grantAgreement//324602/EU/A novel mechanism to regulate gene expression in the brain/DD-PD; BIORXIV: 2023.09.25.559365 |
| DOI: |
10.1101/2023.09.25.559365 |
| Availability: |
https://hal.science/hal-04406124; https://hal.science/hal-04406124v1/document; https://hal.science/hal-04406124v1/file/2023.09.25.559365v2.full.pdf; https://doi.org/10.1101/2023.09.25.559365 |
| Rights: |
https://about.hal.science/hal-authorisation-v1/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.1A6AEF43 |
| Database: |
BASE |