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

2024-09Journal article Open access
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dc.contributor.authorMc Cartney, Ann M.
dc.contributor.authorFormenti, Giulio
dc.contributor.authorMouton, Alice
dc.contributor.authorDe Panis, Diego
dc.contributor.authorMarins, Luísa S.
dc.contributor.authorLeitão, Henrique G.
dc.contributor.authorDiedericks, Genevieve
dc.contributor.authorKirangwa, Joseph
dc.contributor.authorMorselli, Marco
dc.contributor.authorSalces-Ortiz, Judit
dc.contributor.authorEscudero, Nuria
dc.contributor.authorIannucci, Alessio
dc.contributor.authorNatali, Chiara
dc.contributor.authorSvardal, Hannes
dc.contributor.authorFernández, Rosa
dc.contributor.authorDe Pooter, Tim
dc.contributor.authorJoris, Geert
dc.contributor.authorStrazisar, Mojca
dc.contributor.authorWood, Jonathan M. D.
dc.contributor.authorHerron, Katie E.
dc.contributor.authorSeehausen, Ole
dc.contributor.authorWatts, Phillip C.
dc.contributor.authorShaw, Felix
dc.contributor.authorDavey, Robert P.
dc.contributor.authorMinotto, Alice
dc.contributor.authorFernández, José M.
dc.contributor.authorBöhne, Astrid
dc.contributor.authorAlegria, Carla
dc.contributor.authorAlioto, Tyler
dc.contributor.authorAlves, Paulo C.
dc.contributor.authorAmorim, Isabel R.
dc.contributor.authorAury, Jean-Marc
dc.contributor.authorBackstrom, Niclas
dc.contributor.authorBaldrian, Petr
dc.contributor.authorBaltrunaite, Laima
dc.contributor.authorBarta, Endre
dc.contributor.authorBedHom, Bertrand
dc.contributor.authorBelser, Caroline
dc.contributor.authorBergsten, Johannes
dc.contributor.authorBertrand, Laurie
dc.contributor.authorBilandija, Helena
dc.contributor.authorBinzer-Panchal, Mahesh
dc.contributor.authorBista, Iliana
dc.contributor.authorBlaxter, Mark
dc.contributor.authorBorges, Paulo
dc.contributor.authorDias, Guilherme Borges
dc.contributor.authorBosse, Mirte
dc.contributor.authorBrown, Tom
dc.contributor.authorBruggmann, Rémy
dc.contributor.authorBuena-Atienza, Elena
dc.contributor.authorBurgin, Josephine
dc.contributor.authorBuzan, Elena
dc.contributor.authorCariani, Alessia
dc.contributor.authorCasadei, Nicolas
dc.contributor.authorChiara, Matteo
dc.contributor.authorChozas, Sergio
dc.contributor.authorČiampor, Fedor
dc.contributor.authorCrottini, Angelica
dc.contributor.authorCruaud, Corinne
dc.contributor.authorCruz, Fernando
dc.contributor.authorDalen, Love
dc.contributor.authorDe Biase, Alessio
dc.contributor.authordel Campo, Javier
dc.contributor.authorDelic, Teo
dc.contributor.authorDennis, Alice B.
dc.contributor.authorDerks, Martijn F. L.
dc.contributor.authorDiroma, Maria Angela
dc.contributor.authorDjan, Mihajla
dc.contributor.authorDuprat, Simone
dc.contributor.authorEleftheriadi, Klara
dc.contributor.authorFeulner, Philine G. D.
dc.contributor.authorFlot, Jean-François
dc.contributor.authorForni, Giobbe
dc.contributor.authorFosso, Bruno
dc.contributor.authorFournier, Pascal
dc.contributor.authorFournier-Chambrillon, Christine
dc.contributor.authorGabaldon, Toni
dc.contributor.authorGarg, Shilpa
dc.contributor.authorGissi, Carmela
dc.contributor.authorGiupponi, Luca
dc.contributor.authorGomez-Garrido, Jessica
dc.contributor.authorGonzález, Josefa
dc.contributor.authorGrilo, Miguel L.
dc.contributor.authorGrüning, Björn
dc.contributor.authorGuerin, Thomas
dc.contributor.authorGuiglielmoni, Nadege
dc.contributor.authorGut, Marta
dc.contributor.authorHaesler, Marcel P.
dc.contributor.authorHahn, Christoph
dc.contributor.authorHalpern, Balint
dc.contributor.authorHarrison, Peter W.
dc.contributor.authorHeintz, Julia
dc.contributor.authorHindrikson, Maris
dc.contributor.authorHöglund, Jacob
dc.contributor.authorHowe, Kerstin
dc.contributor.authorHughes, Graham M.
dc.contributor.authorIstace, Benjamin
dc.contributor.authorCock, Mark J.
dc.contributor.authorJanžekovič, Franc
dc.contributor.authorJonsson, Zophonias O.
dc.contributor.authorJoye-Dind, Sagane
dc.contributor.authorKoskimäki, Janne J.
dc.contributor.authorKrystufek, Boris
dc.contributor.authorKubacka, Justyna
dc.contributor.authorKuhl, Heiner
dc.contributor.authorKusza, Szilvia
dc.contributor.authorLabadie, Karine
dc.contributor.authorLähteenaro, Meri
dc.contributor.authorLantz, Henrik
dc.contributor.authorLavrinienko, Anton
dc.contributor.authorLeclère, Lucas
dc.contributor.authorLopes, Ricardo Jorge
dc.contributor.authorMadsen, Ole
dc.contributor.authorMagdelenat, Ghislaine
dc.contributor.authorMagoga, Giulia
dc.contributor.authorManousaki, Tereza
dc.contributor.authorMappes, Tapio
dc.contributor.authorMarques, Joao Pedro
dc.contributor.authorRedondo, Gemma I. Martinez
dc.contributor.authorMaumus, Florian
dc.contributor.authorMcCarthy, Shane A.
dc.contributor.authorMegens, Hendrik-Jan
dc.contributor.authorMelo-Ferreira, Jose
dc.contributor.authorMendes, Sofia L.
dc.contributor.authorMontagna, Matteo
dc.contributor.authorMoreno, João
dc.contributor.authorMosbech, Mai-Britt
dc.contributor.authorMoura, Mónica
dc.contributor.authorMusilova, Zuzana
dc.contributor.authorMyers, Eugene
dc.contributor.authorNash, Will J.
dc.contributor.authorNater, Alexander
dc.contributor.authorNicholson, Pamela
dc.contributor.authorNiell, Manuel
dc.contributor.authorNijland, Reindert
dc.contributor.authorNoel, Benjamin
dc.contributor.authorNoren, Karin
dc.contributor.authorOliveira, Pedro H.
dc.contributor.authorOlsen, Remi-Andre
dc.contributor.authorOmetto, Lino
dc.contributor.authorOomen, Rebekah A.
dc.contributor.authorOssowski, Stephan
dc.contributor.authorPalinauskas, Vaidas
dc.contributor.authorPalsson, Snaebjorn
dc.contributor.authorPanibe, Jerome P.
dc.contributor.authorPauperio, Joana
dc.contributor.authorPavlek, Martina
dc.contributor.authorPayen, Emilie
dc.contributor.authorPawlowska, Julia
dc.contributor.authorPellicer, Jaume
dc.contributor.authorPesole, Graziano
dc.contributor.authorPimenta, Joao
dc.contributor.authorPippel, Martin
dc.contributor.authorPirttilä, Anna Maria
dc.contributor.authorPoulakakis, Nikos
dc.contributor.authorRajan, Jeena
dc.contributor.authorM.C. Rego, Rúben
dc.contributor.authorResendes, Roberto
dc.contributor.authorResl, Philipp
dc.contributor.authorRiesgo, Ana
dc.contributor.authorRodin-Morch, Patrik
dc.contributor.authorSoares, Andre E. R.
dc.contributor.authorFernandes, C
dc.contributor.authorRomeiras, Maria M.
dc.contributor.authorRoxo, Guilherme
dc.contributor.authorRüber, Lukas
dc.contributor.authorRuiz-Lopez, Maria Jose
dc.contributor.authorSaarma, Urmas
dc.contributor.authorda Silva, Luis P.
dc.contributor.authorSim-Sim, Manuela
dc.contributor.authorSoler, Lucile
dc.contributor.authorSousa, Vitor C
dc.contributor.authorSantos, Carla Sousa
dc.contributor.authorSpada, Alberto
dc.contributor.authorStefanovic, Milomir
dc.contributor.authorSteger, Viktor
dc.contributor.authorStiller, Josefin
dc.contributor.authorStöck, Matthias
dc.contributor.authorStruck, Torsten H.
dc.contributor.authorSudasinghe, Hiranya
dc.contributor.authorTapanainen, Riikka
dc.contributor.authorTellgren-Roth, Christian
dc.contributor.authorTrindade, Helena
dc.contributor.authorTukalenko, Yevhen
dc.contributor.authorUrso, Ilenia
dc.contributor.authorVacherie, Benoit
dc.contributor.authorVan Belleghem, Steven M.
dc.contributor.authorVan Oers, Kees
dc.contributor.authorVargas-Chavez, Carlos
dc.contributor.authorVelickovic, Nevena
dc.contributor.authorVella, Noel
dc.contributor.authorVella, Adriana
dc.contributor.authorVernesi, Cristiano
dc.contributor.authorVicente, Sara
dc.contributor.authorVilla, Sara
dc.contributor.authorPettersson, Olga Vinnere
dc.contributor.authorVolckaert, Filip A. M.
dc.contributor.authorVoros, Judit
dc.contributor.authorWincker, Patrick
dc.contributor.authorWinkler, Sylke
dc.contributor.authorCiofi, Claudio
dc.contributor.authorWaterhouse, Robert M.
dc.contributor.authorMazzoni, Camila J.
dc.date.accessioned2025-01-06T13:18:31Z
dc.date.available2025-01-06T13:18:31Z
dc.date.issued2024-09
dc.description.abstractA 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.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMc Cartney, A.M., Formenti, G., Mouton, A. et al. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. npj biodivers 3, 28 (2024). https://doi.org/10.1038/s44185-024-00054-6pt_PT
dc.identifier.doi10.1038/s44185-024-00054-6pt_PT
dc.identifier.urihttp://hdl.handle.net/10400.5/96854
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherNaturept_PT
dc.relationThis paper was subject to open peer review by PCI Genomics; see https://genomics.peercommunityin.org/articles/rec?id=298 and would like to acknowledge the PCI reviewers Dr. Justin Ideozu and Dr. Eric Crandall for the time they took to review this manuscript and provide such wonderful feedback. ERGA Infrastructure: We acknowledge access to the storage resources at Barcelona Supercomputing Center. We would like to thank Alisha Ahamed, Josephine Burgin, Joana Paupério, Jeena Rajan and Guy Cochrane from the European Nucleotide Archive (ENA) for their support regarding data coordination and submission. ERGA Hubs: We thank the Antwerp University Hospital Center of Medical Genetics and Jarl Bastianen for access to sequencing library quality control equipment. Commercial Partners: We would like to acknowledge and thank all supplier partners that have kindly donated kits, reagents to the ERGA pilot Library Preparation Hubs to support species without funding to produce the generation of high-quality genomes and annotations. This support has been key to embedding a culture of diversity, equity, inclusion, and justice in the Pilot Project. Specifically we want to thank Dovetail Genomics, Part of Cantata Bio LLC, especially Mark Daly, Thomas Swale and Lily Shuie; Arima Genomics; PacBio; Integrated DNA Technologies (IDT); MagBio Genomics Europe GmbH; Zymo Research; Agilent Technologies; Fisher Scientific Spain; Illumina Inc. ERGA sequencing partners: We would like to thank all the sequencing facilities involved in the project: i) the Integrative Omics platform of the Italian Node of ELIXIR, the European Research Infrastructure for Life Science data, Giovanna Longo for support in library preparation and Apollonia Tullo for the management of the Integrative Omics platform (Italy); ii) the France Génomique network; iii) the DFG-funded NGS Competence Center Tübingen; iv) SciLifeLab Genomics/National Genomics Infrastructure/Uppsala Genome Center and UPPMAX for aiding in High Molecular Weight DNA/RNA extraction, massive parallel sequencing and computational infrastructure; v) we would like to thank all the teams at Wellcome Sanger institute Tree of life programme, namely the ToL Samples management team, the ToL Core Laboratory, the support of Sanger Scientific Operations, especially the Long Read teams, the Tree of Life Assembly team and the Genome Reference Informatics Team, and the Tree of Life ERGA-Pilot project management team, especially Theodora Anderson.; vi) The Earlham Institute by members of the Genomics Pipelines and Core Bioinformatics Groups. This work was also supported by the Scientific Computing group, as well as support for the physical HPC infrastructure and data center delivered via the NBI Research Computing group; vii) the Functional Genomics Center Zurich (FGCZ) for library preparation and sequencing; viii) the NGSP team at the University of Bern, from DNA and RNA extraction to data generation on both long read and short-read platforms; ix) The Lausanne University Genomic Technologies Facility (GTF, Switzerland, https://wp.unil.ch/gtf/) for library preparation and sequencing; x) the DRESDEN concept genome Center, part of the MPI-CBG and the technology platform of the CMCB at the TU Dresden; xi) the DFG Research Infrastructure West German Genome Center. NGS analyses were carried out at the production sites Cologne, Bonn and Düsseldorf; xii) We would like to acknowledge the material support through the Oxford Nanopore Technologies ORG.one project in the execution of sequencing the Acipenser sturio genome at the University of Wageningen (Netherland) xiii) the Centro Nacional de Análisis Genómico CNAG; the Catalan Initiative of the Catalan Biogenome Project; xiv) Computational resources were provided by the HPC core facility CalcUA of the University of Antwerp and VSC (Flemish Supercomputer Center), and the Biomina network. ERGA Training and Knowledge Transfer partners: The 2022 EMBO Practical Course 'Hands-on course in genome sequencing, assembly and downstream analyses' at the Université libre de Bruxelles. Co-authors: L.R would like to thank the Naturhistorisches Museum Bern; D.D.P is funded by Biodiversity Genomics Europe (BGE); The tissue sample for the European mink has been taken from a male mink in Dordogne (France) in 2006 by Pascal Fournier and Christine Fournier-Chambrillon (GREGE, sample collectors), in the framework of the first National Action Plan for the conservation of the European mink, and sent to a collection of cryopreserved cells (managed by Vitaly Volobouev) at MNHN (National Museum of Natural History). This cryopreserved sample was used by Bertrand Bed'Hom (sample ambassador) to generate fresh cell cultures for the production of high-quality DNA by Genoscope, and the construction of a reference genome. The French institutional partners for the European mink conservation programme in France are DREAL (Direction régionale de l’environnement, de l’aménagement et du logement Nouvelle-Aquitaine) and OFB (Office Français de la Biodiversité). ERGA Community: We would like to thank: Svein-Ole Mikalsen and Sunnvør í Kongsstovu (University of Faroe Islands) for the providing Argentina silus and Ammodytes marinus to the pilot project as a of the project Genome Atlas of Faroese Ecology; Michel Sartori (Musée cantonal des sciences naturelles, Lausanne); Karim Gharbi, Suzanne Henderson, Kendall Baker, Tom Barker, Naomi Irish, Jamie McGowan, Will Nash, James Lipscombe, Angela Man, Alex Durrant, Mariano Olivera, Chris Watkins, Jonathan Wright, David Swarbreck, Neil Shearer, Sacha Lucchini, Thomas Brabbs, Vanda Knitlhoffer, Leah Catchpole, Fiona Fraser, Seanna McTaggart (Earlham Institute, Norwich, UK), W.N extracted high molecular weight DNA from Xylocopa violacea individuals, conducted assembly of the resulting PacBio HiFi data, coordinated generation of Hi-C data for this species, and manually curated the scaffolded assembly. LIMS support using SapioLIMS; Lada Jovović (Ruđer Bošković Institute, Croatia); Federica Montesanto and Francesco Mastrototaro (Università degli Studi di Bari 'A. Moro' Dipartimento di Bioscienze, Biotecnologie e Ambiente), for contributing to the design of the Pilot project on two Botryllus species; Jana Bedek (Ruđer Bošković Institute, Croatia); João Jacinto, Helena Trindade, Manuela Sim-Sim (cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa & CHANGE—Global Change and Sustainability Institute, Portugal), M.S.S is Sample Ambassador for Corema album; Christian de Guttry, Julien Marquis (University of Lausanne, Switzerland); Native Flora Centre of Lombardy (Centro Flora Autoctona della Lombardia, CFA), c/o Parco Monte Barro, Galbiate (LC) Italy); Reichlin Pascal; Yannick Chittaro (info fauna); Ferran Palero (Catalan Biogenome Project); Sara Vicente and Cristina Máguas (Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Portugal; Escola Superior de Saúde Ribeiro Sanches (ERISA), IPLUSO—Instituto Politécnico da Lusofonia, Portugal); Maria Judite Alves (Museu Nacional de História Natural e da Ciência, Universidade de Lisboa); Christian Harrison, Dana R. MacGregor (Rothamsted Research) are working with the Earlham Institute to sequence, curate, and annotate an Alopecurus aequalis genome ; Patrik Rödin Mörch (Department of Ecology and Genetics—Animal Ecology, Uppsala University); Björn Marcus von Reumont (Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Applied Bioinformatics Group); Veronique Decroocq (University of Bordeaux, INRAE), Provider of data and samples of Prunus brigantine, Managing sequencing effort on European Prunus species; Lucia Manni, Università di Padova, Dipartimento di Biologia, for contributing to the design of the Pilot project on two Botryllus species; Evan G. Williams (Luxembourg Centre for Systems Biomedicine, University of Luxembourg); Julia Pawłowska (Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Poland); Craig R Primmer (University of Helsinki); Alicja Okrasińska (Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw); Annamaria Giorgi (Centre of Applied Studies for the Sustainable Management and Protection of Mountain Areas-CRC Ge.S.Di.Mont, University of Milan, 25048 Edolo, Italy; Department of Agricultural and Environmental Sciences-Production, Landscape and Agroenergy-DiSAA, University of Milan, 20133 Milan, Italy); Simon Pierce (Department of Agricultural and Environmental Sciences, University of Milan); Shai Meiri (The Steinhardt Museum of Natural History, School of Zoology, Tel Aviv University); Virginia Vanni (Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, United Kingdom); M.M.R. was funded by FCT and AKDN through the project CVAgrobiodiversity/333111699 and (LEAF/ISA) UID/AGR/04129/2020; Akira Peters (Bezhin Rosko, Santec, France) isolated from nature and donated the strain of Phaeosaccion multiseriatum; We would finally like to thank Loriano Ballarin and Fabio Gasparini, Università di Padova, Dipartimento di Biologia, for contributing to the design of the Pilot project of two Botryllus species. We would also like to acknowledge and thank Shane Whelan for his efforts in abstract translation.pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleThe European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomicspt_PT
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