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Draft:The European Reference Genome Atlas

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The European Reference Genome Atlas (ERGA) initiative is a pan-European community aiming to coordinate the production of high-quality reference genomes that represent the entire eukaryotic biodiversity of Europe [1][2]. This involves a collective effort to assemble a growing atlas of reference genomes for all European species including endangered species, keystone species critical for ecosystem function, and other species of special interest to researchers. As the European regional node of the Earth BioGenome Project (EBP[3][4][5]), ERGA collaborates with numerous reference genome projects worldwide and seeks to foster a collaborative network of biodiversity genomics researchers across Europe and beyond.

Summary

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ERGA was launched in 2020, following discussions of the initial concept amongst attendees at the Plant and Animal Genomes (PAG) conference in San Diego, California. The collective writing of a position paper emphasising the importance of reference genomes for biodiversity and ecosystem services conservation and management in Europe served as a catalyst to bring the community together. 2021 saw a period of community formalisation: the establishment of the ERGA Council of representatives from all participating countries; the creation of the ERGA Committees representing the principal stages of the genome generation workflow; the election of the founding chairperson of ERGA; the formation of the first ERGA executive board; and the launch of the ERGA website and membership registration. That year also saw the initiation of the first community call for species nominations to begin to map priorities across Europe, as well as the collaborative work on a forum article[6] published in Trends in Ecology & Evolution on the applications of reference genomes in conservation genomics. The establishment of the community continued through the activities of the ERGA Council and Committees, the setting up of ERGA Core Projects, working on a community review article[7] published in Trends in Genetics, and defining ERGA Phase 1 goals, principles, and participation[1][8].

Goals and principles

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The community-developed strategy aims to promote transnational cooperation by sharing protocols, workflows, and know-how to optimise the applications of the latest genomics technologies in biodiversity research. The main goals are to: [1] Create and consolidate a collaborative and interdisciplinary network of scientists across Europe and associated countries to deliver reference genome sequences; [2] Connect relevant infrastructures across Europe following a distributed model for genome sequence generation and analysis that can increase dynamically; [3] Develop guidelines and best practices for state-of-the-art reference genome sequence generation, and disseminate them through training and knowledge transfer; [4] Connect reference genome initiatives working on European species to maximise synergies. ERGA’s governance centres on the principles of promoting scientific excellence at all levels; building and enhancing distributed expertise and infrastructure; ensuring balanced taxonomic, geographic, and habitat representation; fostering inclusive and socially diverse research practices; adhering to FAIR data guidelines for data generation and sharing; prioritising species that need urgent attention; and supporting the translation of genomics research into practical applications for the benefit of society.{{fact

Projects and activities

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The ERGA Pilot Project [9] was launched in 2021 to test the construction of a distributed network approach to community-driven reference genome generation. Funded and driven by ERGA Members with a bottom-up approach, the Pilot Project aimed to complete at least one high-quality reference genome that reached the Earth Biogenome Project’s assembly metrics [10] from each ERGA-associated country. To establish this decentralised network and to ensure wide participation regardless of access to funding, personnel, and infrastructure, the Pilot Project partnered with 26 sequencing facilities across Europe. Overall, from the 33 countries that participated, 98 species were selected, with each being championed by an international team of genome experts. The Pilot Project helped develop an infrastructure to scale up high-quality reference genome generation, as well as to identify challenges related to ethical and legal compliance as well as equity, diversity, and inclusion.[citation needed]

Launched in September 2022, the Horizon Europe funded Biodiversity Genomics Europe (BGE) Project [11], a joint endeavour between the ERGA and the International Barcode of Life (iBOL) Europe [12] communities. The BGE Project aims to accelerate the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. Through BGE, ERGA continues to build the distributed network approach by testing and developing guidelines and best practices for state-of-the-art reference genome sequence generation and connecting relevant infrastructures and stakeholders across Europe.{{fact

Genomic resources for European species whose generation benefited from support and/or materials offered through the ERGA Committees and the BGE Project can be formally recognised as ERGA Community Genomes [13] that meet recognised reference-quality standards.

ERGA launched the ERGA Knowledge Hub [14] in June 2024. This portal aims to gather and share educational materials on genomics and related topics, lowering access barriers and promoting knowledge exchange across Europe and beyond. The catalogue of educational material collected at the ERGA Knowledge Hub is collated from community input following curation to ensure the quality and relevance of the content.{{fact

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References

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  1. ^ a b Mazzoni, Camila J.; Ciofi, Claudio; Waterhouse, Robert M. (2023-07-11). "Biodiversity: an atlas of European reference genomes". Nature. 619 (7969): 252. Bibcode:2023Natur.619..252M. doi:10.1038/d41586-023-02229-w. PMID 37433931.
  2. ^ "A genome atlas of european biodiversity". erga. Retrieved 2024-08-23.
  3. ^ Lewin, Harris A.; Robinson, Gene E.; Kress, W. John; Baker, William J.; Coddington, Jonathan; Crandall, Keith A.; Durbin, Richard; Edwards, Scott V.; Forest, Félix; Gilbert, M. Thomas P.; Goldstein, Melissa M.; Grigoriev, Igor V.; Hackett, Kevin J.; Haussler, David; Jarvis, Erich D. (2018-04-24). "Earth BioGenome Project: Sequencing life for the future of life". Proceedings of the National Academy of Sciences. 115 (17): 4325–4333. Bibcode:2018PNAS..115.4325L. doi:10.1073/pnas.1720115115. ISSN 0027-8424. PMC 5924910. PMID 29686065.
  4. ^ Lewin, Harris A.; Richards, Stephen; Lieberman Aiden, Erez; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine B.; Baumgartner, Bridget; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark L.; Cai, Jing; Caperello, Nicolette D.; Carlson, Keith; Castilla-Rubio, Juan Carlos (2022-01-25). "The Earth BioGenome Project 2020: Starting the clock". Proceedings of the National Academy of Sciences. 119 (4). Bibcode:2022PNAS..11915635L. doi:10.1073/pnas.2115635118. ISSN 0027-8424. PMC 8795548. PMID 35042800.
  5. ^ "Earth BioGenome Project". Earth BioGenome Project. Retrieved 2024-08-23.
  6. ^ Formenti, Giulio; Theissinger, Kathrin; Fernandes, Carlos; Bista, Iliana; Bombarely, Aureliano; Bleidorn, Christoph; Ciofi, Claudio; Crottini, Angelica; Godoy, José A.; Höglund, Jacob; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A.; Paez, Sadye; Palsbøll, Per J. (March 2022). "The era of reference genomes in conservation genomics". Trends in Ecology & Evolution. 37 (3): 197–202. Bibcode:2022TEcoE..37..197F. doi:10.1016/j.tree.2021.11.008. ISSN 0169-5347. PMID 35086739.
  7. ^ Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul R.; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R.; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A.; Paez, Sadye (July 2023). "How genomics can help biodiversity conservation". Trends in Genetics. 39 (7): 545–559. doi:10.1016/j.tig.2023.01.005. ISSN 0168-9525. PMID 36801111.
  8. ^ ERGA Council, Aghayan, S. A., Alvarez, N., Baldrian, P., Baltrunaite, L., Barta, E., Bista, I., Böhne, A., Bonisoli-Alquati, A., Buzan, E., Čiampor Jr, F., Ciofi, C., Corominas, M., Djan, M., Fernández, R., Feulner, P. G. D., Flouri, T., Formenti, G., Gissi, C., … Mazzoni, C. J. (2023). European Reference Genome Atlas Community - Phase 1 Members - 2020-2023 (Version1-2023-06-27) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8083652
  9. ^ Cartney, Ann M. Mc; Formenti, Giulio; Mouton, Alice; Panis, Diego De; Marins, Luisa S.; Leitao, Henrique G.; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco (2024-03-25), The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics, doi:10.1101/2023.09.25.559365, retrieved 2024-08-23
  10. ^ Lawniczak, Mara K. N.; Durbin, Richard; Flicek, Paul; Lindblad-Toh, Kerstin; Wei, Xiaofeng; Archibald, John M.; Baker, William J.; Belov, Katherine; Blaxter, Mark L.; Marques Bonet, Tomas; Childers, Anna K.; Coddington, Jonathan A.; Crandall, Keith A.; Crawford, Andrew J.; Davey, Robert P. (2022-01-25). "Standards recommendations for the Earth BioGenome Project". Proceedings of the National Academy of Sciences. 119 (4). Bibcode:2022PNAS..11915639L. doi:10.1073/pnas.2115639118. ISSN 0027-8424. PMC 8795494. PMID 35042802.
  11. ^ Genomics, Biodiversity. "BGE Home". Biodiversity Genomics Europe. Retrieved 2024-08-23.
  12. ^ Europe, iBOL. "Homepage". iBOL Europe. Retrieved 2024-08-23.
  13. ^ "ERGA Community genomes (beta)". ERGA. Retrieved 2024-08-23.
  14. ^ "ERGA Knowledge Hub- Training material for Biodiversity Genomics". knowledge.erga-biodiversity.eu. Retrieved 2024-08-23.
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