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Preprints, Working Papers, ... Year : 2023

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

Ann M Mc Cartney (1) , 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 , Jo 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 Bed’hom (2) , Caroline Belser , Johannes Bergsten , Laurie Bertrand , Helena Bilandžija , Mahesh Binzer-Panchal , Iliana Bista , Mark Blaxter , Paulo Av Borges , Guilherme Borges Dias , Mirte Bosse , Tom Brown , Rémy Bruggmann , Elena Buena-Atienza , Josephine Burgin , Elena Buzan , Nicolas Casadei , Matteo Chiara , Sergio Chozas , Fedor Čiampor , Angelica Crottini , Corinne Cruaud , Fernando Cruz , Love Dalen , Alessio de Biase , Javier del Campo , Teo Delić , Alice B Dennis , Martijn Fl Derks , Maria Angela Diroma , Mihajla Djan , Simone Duprat , Klara Eleftheriadi , Philine Gd Feulner , Jean-François Flot , Giobbe Forni , Bruno Fosso , Pascal Fournier , Christine Fournier-Chambrillon , Toni Gabaldon , Shilpa Garg , Carmela Gissi , Luca Giupponi , Jèssica Gómez-Garrido , Josefa González , Miguel L Grilo , Bjoern Gruening , Thomas Guérin , Nadège Guiglielmoni , Marta Gut , Marcel P Haesler , Christoph Hahn , Balint Halpern , Peter Harrison , Julia Heintz , Maris Hindrikson , Jacob Höglund , Kerstin Howe , Graham Hughes , Benjamin Istace , Mark J Cock (3, 4, 5, 6) , Franc Jancekovic , Zophonías O Jónsson , Sagane Joye-Dind , Janne J Koskimaki , Boris Krystufek , Justyna Kubacka , Heiner Kuhl , Szilvia Kusza , Karine Labadie , Meri Lahteenaro , Henrik Lantz , Anton Lavrinienko , Lucas Leclère , Ricardo Jorge Lopes , Ole Madsen , Ghislaine Magdelenat , Giulia Magoga , Tereza Manousaki , Tapio Mappes , João P Marques , Gemma I Martinez Redondo , Florian Maumus , Hendrik-Jan Megens , José Melo-Ferreira , Sofia L Mendes , Matteo Montagna , João Moreno , Mai-Britt Mosbech , Monica Moura , Zuzana Musilova , Eugene Myers , Will J Nash , Alexander Nater , Pamela Nicholson , Manuel Niell , Reindert Nijland , Benjamin Noel , Karin Norén , Pedro H. Oliveira (7, 8, 9) , Remi-Andre Olsen , Lino Ometto , Stephan Ossowski , Vaidas Palinauskas , Snæbjörn Pálsson , Jerome P Panibe , Joana Paupério , Martina Pavlek , Emilie Payen , Julia Pawłowska , Jaume Pellicer , Graziano Pesole , Joao Pimenta , Martin Pippel , Anna Maria Pirttilä , Nikos Poulakakis , Jeena Rajan , Ruben Mc Rego , Roberto Resendes , Philipp Resl , Ana Riesgo , Patrik Rödin-Mörch , André Er Soares , Carlos Rodríguez Fernandes , Maria M Romeiras , Guilherme Roxo , Lukas Ruber , María José Ruiz-López , Urmas Saarma , Luis P Silva , Manuela Sim-Sim , Lucile Soler , Vitor C Sousa , Carla Sousa Santos , Alberto Spada , Milomir Stefanović , Viktor Steger , Josefin Stiller , Matthias Stöck , Torsten Hugo 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 Am Volckaert , Judit Vörös , Patrick Wincker , Sylke Winkler , Claudio Ciofi , Robert M Waterhouse , Camila J Mazzoni
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
  • Function : Author
Mojca Strazisar
Jo 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
Caroline Belser
Johannes Bergsten
Laurie Bertrand
Helena Bilandžija
Mahesh Binzer-Panchal
Iliana Bista
Mark Blaxter
Paulo Av Borges
Guilherme Borges Dias
Mirte Bosse
Tom Brown
Rémy Bruggmann
Elena Buena-Atienza
Josephine Burgin
Elena Buzan
Nicolas Casadei
Matteo Chiara
Sergio Chozas
Fedor Čiampor
Angelica Crottini
Corinne Cruaud
Fernando Cruz
Love Dalen
Alessio de Biase
Javier del Campo
Teo Delić
Alice B Dennis
Martijn Fl Derks
Maria Angela Diroma
Mihajla Djan
Simone Duprat
  • Function : Author
Klara Eleftheriadi
Philine Gd Feulner
Jean-François Flot
Giobbe Forni
Bruno Fosso
Pascal Fournier
  • Function : Author
Christine Fournier-Chambrillon
Toni Gabaldon
Shilpa Garg
Carmela Gissi
Luca Giupponi
Jèssica Gómez-Garrido
Josefa González
Miguel L Grilo
Bjoern Gruening
Thomas Guérin
Nadège Guiglielmoni
Marta Gut
Marcel P Haesler
  • Function : Author
Christoph Hahn
Balint Halpern
Peter Harrison
Julia Heintz
Maris Hindrikson
Jacob Höglund
Kerstin Howe
Graham Hughes
Benjamin Istace
Franc Jancekovic
Zophonías O Jónsson
Sagane Joye-Dind
Janne J Koskimaki
Boris Krystufek
Justyna Kubacka
Heiner Kuhl
Szilvia Kusza
Karine Labadie
Meri Lahteenaro
Henrik Lantz
Anton Lavrinienko
Lucas Leclère
Ricardo Jorge Lopes
Ole Madsen
Ghislaine Magdelenat
Giulia Magoga
Tereza Manousaki
Tapio Mappes
João P Marques
Gemma I Martinez Redondo
Florian Maumus
Hendrik-Jan Megens
José Melo-Ferreira
Sofia L Mendes
Matteo Montagna
João Moreno
Mai-Britt Mosbech
Monica Moura
Zuzana Musilova
Eugene Myers
Will J Nash
Alexander Nater
Pamela Nicholson
Manuel Niell
Reindert Nijland
Benjamin Noel
Karin Norén
Remi-Andre Olsen
Lino Ometto
Stephan Ossowski
Vaidas Palinauskas
Snæbjörn Pálsson
Jerome P Panibe
Joana Paupério
Martina Pavlek
Emilie Payen
Julia Pawłowska
Jaume Pellicer
Graziano Pesole
Joao Pimenta
Martin Pippel
Anna Maria Pirttilä
Nikos Poulakakis
Jeena Rajan
Ruben Mc Rego
Roberto Resendes
Philipp Resl
Ana Riesgo
Patrik Rödin-Mörch
André Er Soares
Carlos Rodríguez Fernandes
Maria M Romeiras
Guilherme Roxo
Lukas Ruber
María José Ruiz-López
Urmas Saarma
Luis P Silva
Manuela Sim-Sim
Lucile Soler
Vitor C Sousa
Carla Sousa Santos
Alberto Spada
Milomir Stefanović
Viktor Steger
Josefin Stiller
Matthias Stöck
Torsten Hugo 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 Am Volckaert
Judit Vörös
Patrick Wincker
Sylke Winkler
Claudio Ciofi
Robert M Waterhouse
Camila J Mazzoni

Abstract

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.
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Dates and versions

hal-04406124 , version 1 (19-01-2024)

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Ann M Mc Cartney, Giulio Formenti, Alice Mouton, Diego de Panis, Luísa S Marins, et al.. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. 2024. ⟨hal-04406124⟩
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