The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics-Reference-Cited by-同舟云学术

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

Published:2023-09-28 Issue: Volume: Page:
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Mc Cartney Ann M^ORCID,Formenti Giulio^ORCID,Mouton Alice^ORCID,De Panis Diego^ORCID,Marins Luísa S^ORCID,Leitão Henrique G^ORCID,Diedericks Genevieve^ORCID,Kirangwa Joseph^ORCID,Morselli Marco^ORCID,Salces-Ortiz Judit^ORCID,Escudero Nuria^ORCID,Iannucci Alessio^ORCID,Natali Chiara^ORCID,Svardal Hannes^ORCID,Fernández Rosa^ORCID,De Pooter Tim^ORCID,Joris Geert,Strazisar Mojca^ORCID,Wood Jo^ORCID,Herron Katie E^ORCID,Seehausen Ole^ORCID,Watts Phillip C^ORCID,Shaw Felix^ORCID,Davey Robert P^ORCID,Minotto Alice^ORCID,Fernández José M^ORCID,Böhne Astrid^ORCID,Alegria Carla^ORCID,Alioto Tyler^ORCID,Alves Paulo C^ORCID,Amorim Isabel R^ORCID,Aury Jean-Marc^ORCID,Backstrom Niclas^ORCID,Baldrian Petr^ORCID,Baltrunaite Laima^ORCID,Barta Endre^ORCID,Bed’Hom Bertrand^ORCID,Belser Caroline^ORCID,Bergsten Johannes^ORCID,Bertrand Laurie^ORCID,Bilandžija Helena^ORCID,Binzer-Panchal Mahesh^ORCID,Bista Iliana^ORCID,Blaxter Mark^ORCID,Borges Paulo AV^ORCID,Borges Dias Guilherme^ORCID,Bosse Mirte^ORCID,Brown Tom^ORCID,Bruggmann Rémy^ORCID,Buena-Atienza Elena^ORCID,Burgin Josephine^ORCID,Buzan Elena^ORCID,Casadei Nicolas^ORCID,Chiara Matteo^ORCID,Chozas Sergio^ORCID,Čiampor Fedor^ORCID,Crottini Angelica^ORCID,Cruaud Corinne^ORCID,Cruz Fernando^ORCID,Dalen Love^ORCID,De Biase Alessio^ORCID,del Campo Javier^ORCID,Delić Teo^ORCID,Dennis Alice B^ORCID,Derks Martijn FL^ORCID,Diroma Maria Angela^ORCID,Djan Mihajla^ORCID,Duprat Simone,Eleftheriadi Klara^ORCID,Feulner Philine GD^ORCID,Flot Jean-François^ORCID,Forni Giobbe^ORCID,Fosso Bruno^ORCID,Fournier Pascal,Fournier-Chambrillon Christine^ORCID,Gabaldon Toni^ORCID,Garg Shilpa^ORCID,Gissi Carmela^ORCID,Giupponi Luca^ORCID,Gómez-Garrido Jèssica^ORCID,González Josefa^ORCID,Grilo Miguel L^ORCID,Gruening Bjoern^ORCID,Guérin Thomas^ORCID,Guiglielmoni Nadège^ORCID,Gut Marta^ORCID,Haesler Marcel P,Hahn Christoph^ORCID,Halpern Balint^ORCID,Harrison Peter^ORCID,Heintz Julia^ORCID,Hindrikson Maris^ORCID,Höglund Jacob^ORCID,Howe Kerstin^ORCID,Hughes Graham^ORCID,Istace Benjamin^ORCID,Cock Mark J.^ORCID,Jancekovic Franc^ORCID,Jónsson Zophonías O^ORCID,Joye-Dind Sagane^ORCID,Koskimaki Janne J.^ORCID,Krystufek Boris^ORCID,Kubacka Justyna^ORCID,Kuhl Heiner^ORCID,Kusza Szilvia^ORCID,Labadie Karine^ORCID,Lahteenaro Meri^ORCID,Lantz Henrik^ORCID,Lavrinienko Anton^ORCID,Leclère Lucas^ORCID,Lopes Ricardo Jorge^ORCID,Madsen Ole^ORCID,Magdelenat Ghislaine^ORCID,Magoga Giulia^ORCID,Manousaki Tereza^ORCID,Mappes Tapio^ORCID,Marques João P^ORCID,Martinez Redondo Gemma I^ORCID,Maumus Florian^ORCID,Megens Hendrik-Jan^ORCID,Melo-Ferreira José^ORCID,Mendes Sofia L^ORCID,Montagna Matteo^ORCID,Moreno João^ORCID,Mosbech Mai-Britt^ORCID,Moura Monica^ORCID,Musilova Zuzana^ORCID,Myers Eugene^ORCID,Nash Will J.^ORCID,Nater Alexander^ORCID,Nicholson Pamela^ORCID,Niell Manuel^ORCID,Nijland Reindert^ORCID,Noel Benjamin^ORCID,Norén Karin^ORCID,Oliveira Pedro H^ORCID,Olsen Remi-Andre^ORCID,Ometto Lino^ORCID,Ossowski Stephan^ORCID,Palinauskas Vaidas^ORCID,Pálsson Snæbjörn^ORCID,Panibe Jerome P^ORCID,Paupério Joana^ORCID,Pavlek Martina^ORCID,Payen Emilie^ORCID,Pawłowska Julia^ORCID,Pellicer Jaume^ORCID,Pesole Graziano^ORCID,Pimenta Joao^ORCID,Pippel Martin^ORCID,Pirttilä Anna Maria^ORCID,Poulakakis Nikos^ORCID,Rajan Jeena^ORCID,Rego Ruben MC^ORCID,Resendes Roberto^ORCID,Resl Philipp^ORCID,Riesgo Ana^ORCID,Rödin-Mörch Patrik^ORCID,Soares André ER^ORCID,Rodríguez Fernandes Carlos^ORCID,Romeiras Maria M.^ORCID,Roxo Guilherme^ORCID,Ruber Lukas^ORCID,Ruiz-López María José^ORCID,Saarma Urmas^ORCID,Silva Luis P^ORCID,Sim-Sim Manuela^ORCID,Soler Lucile^ORCID,Sousa Vitor C^ORCID,Sousa Santos Carla^ORCID,Spada Alberto^ORCID,Stefanović Milomir^ORCID,Steger Viktor^ORCID,Stiller Josefin^ORCID,Stöck Matthias^ORCID,Struck Torsten Hugo H^ORCID,Sudasinghe Hiranya^ORCID,Tapanainen Riikka^ORCID,Tellgren-Roth Christian^ORCID,Trindade Helena^ORCID,Tukalenko Yevhen^ORCID,Urso Ilenia^ORCID,Vacherie Benoit^ORCID,Van Belleghem Steven M^ORCID,van Oers Kees^ORCID,Vargas-Chavez Carlos^ORCID,Velickovic Nevena^ORCID,Vella Noel^ORCID,Vella Adriana^ORCID,Vernesi Cristiano^ORCID,Vicente Sara^ORCID,Villa Sara^ORCID,Vinnere Pettersson Olga^ORCID,Volckaert Filip AM^ORCID,Vörös Judit^ORCID,Wincker Patrick^ORCID,Winkler Sylke^ORCID,Ciofi Claudio^ORCID,Waterhouse Robert M^ORCID,Mazzoni Camila J^ORCID

Abstract

AbstractA 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.

Publisher

Cold Spring Harbor Laboratory

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