Draft:The European Reference Genome Atlas
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The European Reference Genome Atlas (ERGA) is a community initiative coordinating the production of a reference genome for all eukaryotic species in Europe [1][2]. This involves field sampling and DNA sequencing, followed by sequence assembly and annotation, to generate a catalogue of genomes that meet reference quality standards[3]. As the European regional node of the Earth BioGenome Project (EBP[4][5]), ERGA collaborates with other genome projects worldwide, such as the African BioGenome Project[6] and the Vertebrate Genomes Project[7], to foster a network of biodiversity genomics researchers across Europe and beyond.
Background
[edit]Researchers worldwide recognise the needs and opportunities for genomics to support biodiversity and ecosystem services conservation and management [8][9] . In response, ERGA was launched in 2020 to build a European initiative with a focus on reference genome production. Community formalisation included establishing the Council of representatives from all participating countries and setting up the Committees to oversee the main stages of the genome generation workflow. Community establishment continued through activities of the Council and Committees, setting up of Core Projects, partnering with technology providers such as Pacific BioSciences [10] and Arima Genomics [11], publication of a forum article [12] and a community review article [13], as well as defining the goals, principles, and participation of the ERGA community [1][14]. Core Projects include the Pilot Project [15], aiming to complete at least one reference genome from each ERGA-associated country, and the Horizon Europe funded Biodiversity Genomics Europe Project [16], a joint endeavour with the International Barcode of Life Europe community[17], as well as building the ERGA Knowledge Hub [18] that gathers and shares educational materials on biodiversity genomics and related topics to promote knowledge exchange.
External links
[edit]- The European Reference Genome Atlas (ERGA)
- The Earth BioGenome Project (EBP)
- The 5,000 Arthropod Genomes Initiative (i5k)
- The Bird 10,000 Genomes (B10K) Project
- The Darwin Tree of Life (DToL) Project
- The Earth BioGenome Project Norway (EBP-Nor)
- ATLASea, an atlas of marine genomes
- The Catalan Initiative for the Earth Biogenome Project (CBP)
- The African BioGenome Project (AfricaBP)
- The Vertebrate Genomes Project (VGP)
- The Biodiversity Genomics Europe (BGE) Project
- The Australian Threatened Species Initiative (TSI)
References
[edit]- ^ a b Mazzoni, Camila J.; Ciofi, Claudio; Waterhouse, Robert M. (2023-07-11). "Biodiversity: an atlas of European reference genomes". Nature. 619 (7969): 252. doi:10.1038/d41586-023-02229-w. PMID 37433931.
- ^ "A genome atlas of european biodiversity". erga. Retrieved 2024-11-21.
- ^ 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). doi:10.1073/pnas.2115639118. ISSN 0027-8424. PMC 8795494. PMID 35042802.
- ^ 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. doi:10.1073/pnas.1720115115. ISSN 0027-8424. PMC 5924910. PMID 29686065.
- ^ 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). doi:10.1073/pnas.2115635118. ISSN 0027-8424. PMC 8795548. PMID 35042800.
- ^ "100,000 genomes — in Africa, for Africa". Nature Biotechnology. 40 (7): 988. 2022-07-01. doi:10.1038/s41587-022-01404-0. ISSN 1546-1696. PMID 35831666.
- ^ Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier; Damas, Joana; Formenti, Giulio; Koren, Sergey; Uliano-Silva, Marcela; Chow, William; Fungtammasan, Arkarachai; Kim, Juwan; Lee, Chul; Ko, Byung June; Chaisson, Mark; Gedman, Gregory L.; Cantin, Lindsey J. (April 2021). "Towards complete and error-free genome assemblies of all vertebrate species". Nature. 592 (7856): 737–746. doi:10.1038/s41586-021-03451-0. ISSN 1476-4687.
- ^ Heuertz, Myriam; Carvalho, Silvia B.; Galindo, Juan; Rinkevich, Baruch; Robakowski, Piotr; Aavik, Tsipe; Altinok, Ilhan; Barth, Julia M. I.; Cotrim, Helena; Goessen, Roos; González-Martínez, Santiago C.; Grebenc, Tine; Hoban, Sean; Kopatz, Alexander; McMahon, Barry J. (2023-02-01). "The application gap: Genomics for biodiversity and ecosystem service management". Biological Conservation. 278: 109883. doi:10.1016/j.biocon.2022.109883. ISSN 0006-3207.
- ^ Hogg, Carolyn J. (May 2024). "Translating genomic advances into biodiversity conservation". Nature Reviews Genetics. 25 (5): 362–373. doi:10.1038/s41576-023-00671-0. ISSN 1471-0064. PMID 38012268.
- ^ "PacBio Partners with the European Reference Genome Atlas Initiative". PacBio. Retrieved 2024-11-21.
- ^ "Arima Genomics and European Reference Genome Atlas Join Forces to Preserve Biodiversity". Arima Genomics. Retrieved 2024-11-21.
- ^ 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. doi:10.1016/j.tree.2021.11.008. ISSN 0169-5347. PMID 35086739.
- ^ 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.
- ^ ERGA Council; et al. (2023). "European Reference Genome Atlas Community - Phase 1 Members - 2020-2023". doi:10.5281/zenodo.8083652.
- ^ 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 (2024-09-17). "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics". npj Biodiversity. 3 (1): 1–17. doi:10.1038/s44185-024-00054-6. ISSN 2731-4243.
- ^ Genomics, Biodiversity. "BGE Home". Biodiversity Genomics Europe. Retrieved 2024-11-21.
- ^ Europe, iBOL. "iBOL Europe – European node of the International Barcode of Life". iBOL Europe. Retrieved 2024-11-21.
- ^ "ERGA Knowledge Hub- Training material for Biodiversity Genomics". knowledge.erga-biodiversity.eu. Retrieved 2024-11-21.
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