European Reference Genome Atlas
{{Short description|Genome project cataloging Europe's eukaryotic species}}
The European Reference Genome Atlas (ERGA) is a community initiative coordinating the production of a reference genome for all eukaryotic species in Europe.{{Cite journal |last=Mazzoni |first=Camila J. |last2=Ciofi |first2=Claudio |last3=Waterhouse |first3=Robert M. |date=2023-07-11 |title=Biodiversity: an atlas of European reference genomes |url=https://www.nature.com/articles/d41586-023-02229-w |journal=Nature |language=en |volume=619 |issue=7969 |pages=252 |doi=10.1038/d41586-023-02229-w |pmid=37433931|url-access=subscription }}{{Cite web |title=A genome atlas of european biodiversity |url=https://www.erga-biodiversity.eu/ |access-date=2024-11-21 |website=erga |language=en}} This involves field sampling and DNA sequencing, followed by sequence assembly and annotation, to generate a catalogue of genomes that meet reference quality standards.{{Cite journal |last=Lawniczak |first=Mara K. N. |last2=Durbin |first2=Richard |last3=Flicek |first3=Paul |last4=Lindblad-Toh |first4=Kerstin |last5=Wei |first5=Xiaofeng |last6=Archibald |first6=John M. |last7=Baker |first7=William J. |last8=Belov |first8=Katherine |last9=Blaxter |first9=Mark L. |last10=Marques Bonet |first10=Tomas |last11=Childers |first11=Anna K. |last12=Coddington |first12=Jonathan A. |last13=Crandall |first13=Keith A. |last14=Crawford |first14=Andrew J. |last15=Davey |first15=Robert P. |date=2022-01-25 |title=Standards recommendations for the Earth BioGenome Project |journal=Proceedings of the National Academy of Sciences |language=en |volume=119 |issue=4 |doi=10.1073/pnas.2115639118 |issn=0027-8424 |pmc=8795494 |pmid=35042802 |doi-access=free}} As the European regional node of the Earth BioGenome Project (EBP{{Cite journal |last=Lewin |first=Harris A. |last2=Robinson |first2=Gene E. |last3=Kress |first3=W. John |last4=Baker |first4=William J. |last5=Coddington |first5=Jonathan |last6=Crandall |first6=Keith A. |last7=Durbin |first7=Richard |last8=Edwards |first8=Scott V. |last9=Forest |first9=Félix |last10=Gilbert |first10=M. Thomas P. |last11=Goldstein |first11=Melissa M. |last12=Grigoriev |first12=Igor V. |last13=Hackett |first13=Kevin J. |last14=Haussler |first14=David |last15=Jarvis |first15=Erich D. |date=2018-04-24 |title=Earth BioGenome Project: Sequencing life for the future of life |journal=Proceedings of the National Academy of Sciences |language=en |volume=115 |issue=17 |pages=4325–4333 |doi=10.1073/pnas.1720115115 |issn=0027-8424 |pmc=5924910 |pmid=29686065 |doi-access=free}}{{Cite journal |last=Lewin |first=Harris A. |last2=Richards |first2=Stephen |last3=Lieberman Aiden |first3=Erez |last4=Allende |first4=Miguel L. |last5=Archibald |first5=John M. |last6=Bálint |first6=Miklós |last7=Barker |first7=Katharine B. |last8=Baumgartner |first8=Bridget |last9=Belov |first9=Katherine |last10=Bertorelle |first10=Giorgio |last11=Blaxter |first11=Mark L. |last12=Cai |first12=Jing |last13=Caperello |first13=Nicolette D. |last14=Carlson |first14=Keith |last15=Castilla-Rubio |first15=Juan Carlos |date=2022-01-25 |title=The Earth BioGenome Project 2020: Starting the clock |journal=Proceedings of the National Academy of Sciences |language=en |volume=119 |issue=4 |doi=10.1073/pnas.2115635118 |issn=0027-8424 |pmc=8795548 |pmid=35042800 |doi-access=free}}), ERGA collaborates with other genome projects worldwide, such as the African BioGenome Project{{Cite journal |date=2022-07-01 |title=100,000 genomes — in Africa, for Africa |url=https://www.nature.com/articles/s41587-022-01404-0 |journal=Nature Biotechnology |language=en |volume=40 |issue=7 |pages=988 |doi=10.1038/s41587-022-01404-0 |issn=1546-1696 |pmid=35831666|url-access=subscription }} and the Vertebrate Genomes Project{{Cite journal |last=Rhie |first=Arang |last2=McCarthy |first2=Shane A. |last3=Fedrigo |first3=Olivier |last4=Damas |first4=Joana |last5=Formenti |first5=Giulio |last6=Koren |first6=Sergey |last7=Uliano-Silva |first7=Marcela |last8=Chow |first8=William |last9=Fungtammasan |first9=Arkarachai |last10=Kim |first10=Juwan |last11=Lee |first11=Chul |last12=Ko |first12=Byung June |last13=Chaisson |first13=Mark |last14=Gedman |first14=Gregory L. |last15=Cantin |first15=Lindsey J. |date=April 2021 |title=Towards complete and error-free genome assemblies of all vertebrate species |url=https://www.nature.com/articles/s41586-021-03451-0 |journal=Nature |language=en |volume=592 |issue=7856 |pages=737–746 |doi=10.1038/s41586-021-03451-0 |issn=1476-4687|hdl=10230/48169 |hdl-access=free }}
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Background
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{{Cite journal |last=Heuertz |first=Myriam |last2=Carvalho |first2=Silvia B. |last3=Galindo |first3=Juan |last4=Rinkevich |first4=Baruch |last5=Robakowski |first5=Piotr |last6=Aavik |first6=Tsipe |last7=Altinok |first7=Ilhan |last8=Barth |first8=Julia M. I. |last9=Cotrim |first9=Helena |last10=Goessen |first10=Roos |last11=González-Martínez |first11=Santiago C. |last12=Grebenc |first12=Tine |last13=Hoban |first13=Sean |last14=Kopatz |first14=Alexander |last15=McMahon |first15=Barry J. |date=2023-02-01 |title=The application gap: Genomics for biodiversity and ecosystem service management |url=https://www.sciencedirect.com/science/article/pii/S0006320722004360 |journal=Biological Conservation |volume=278 |pages=109883 |doi=10.1016/j.biocon.2022.109883 |issn=0006-3207|hdl=10449/79175 |hdl-access=free }}{{Cite journal |last=Hogg |first=Carolyn J. |date=May 2024 |title=Translating genomic advances into biodiversity conservation |url=https://www.nature.com/articles/s41576-023-00671-0 |journal=Nature Reviews Genetics |language=en |volume=25 |issue=5 |pages=362–373 |doi=10.1038/s41576-023-00671-0 |issn=1471-0064 |pmid=38012268|url-access=subscription }} {{Cite web |title=PacBio Partners with the European Reference Genome Atlas Initiative |url=https://www.pacb.com/press_releases/pacbio-partners-with-the-european-reference-genome-atlas-initiative/ |access-date=2024-11-21 |website=PacBio |language=en-US}} and Arima Genomics,{{Cite web |title=Arima Genomics and European Reference Genome Atlas Join Forces to Preserve Biodiversity |url=https://arimagenomics.com/press/arima-genomics-and-european-reference-genome-atlas-join-forces-to-preserve-biodiversity/ |access-date=2024-11-21 |website=Arima Genomics |language=en-US}} publication of a forum article{{Cite journal |last=Formenti |first=Giulio |last2=Theissinger |first2=Kathrin |last3=Fernandes |first3=Carlos |last4=Bista |first4=Iliana |last5=Bombarely |first5=Aureliano |last6=Bleidorn |first6=Christoph |last7=Ciofi |first7=Claudio |last8=Crottini |first8=Angelica |last9=Godoy |first9=José A. |last10=Höglund |first10=Jacob |last11=Malukiewicz |first11=Joanna |last12=Mouton |first12=Alice |last13=Oomen |first13=Rebekah A. |last14=Paez |first14=Sadye |last15=Palsbøll |first15=Per J. |date=March 2022 |title=The era of reference genomes in conservation genomics |url=https://linkinghub.elsevier.com/retrieve/pii/S016953472100313X |journal=Trends in Ecology & Evolution |volume=37 |issue=3 |pages=197–202 |doi=10.1016/j.tree.2021.11.008 |issn=0169-5347 |pmid=35086739|hdl=10230/52728 |hdl-access=free }} and a community review article,{{Cite journal |last=Theissinger |first=Kathrin |last2=Fernandes |first2=Carlos |last3=Formenti |first3=Giulio |last4=Bista |first4=Iliana |last5=Berg |first5=Paul R. |last6=Bleidorn |first6=Christoph |last7=Bombarely |first7=Aureliano |last8=Crottini |first8=Angelica |last9=Gallo |first9=Guido R. |last10=Godoy |first10=José A. |last11=Jentoft |first11=Sissel |last12=Malukiewicz |first12=Joanna |last13=Mouton |first13=Alice |last14=Oomen |first14=Rebekah A. |last15=Paez |first15=Sadye |date=July 2023 |title=How genomics can help biodiversity conservation |url=https://linkinghub.elsevier.com/retrieve/pii/S0168952523000203 |journal=Trends in Genetics |volume=39 |issue=7 |pages=545–559 |doi=10.1016/j.tig.2023.01.005 |issn=0168-9525 |pmid=36801111|hdl=10230/59627 |hdl-access=free }} as well as defining the goals, principles, and participation of the ERGA community.{{Cite web |last=ERGA Council |last2=Aghayan |first2=Sargis Aghasi |last3=Alvarez |first3=Nadir |last4=Baldrian |first4=Petr |last5=Baltrunaite |first5=Laima |last6=Barta |first6=Endre |last7=Bista |first7=Iliana |last8=Böhne |first8=Astrid |last9=Bonisoli-Alquati |first9=Andrea |last10=Buzan |first10=Elena |last11=Čiampor Jr |first11=Fedor |last12=Ciofi |first12=Claudio |last13=Corominas |first13=Montserrat |last14=Djan |first14=Mihajla |last15=Fernández |first15=Rosa |display-authors=1 |date=2023 |title=European Reference Genome Atlas Community - Phase 1 Members - 2020-2023 |url=https://zenodo.org/records/8083652 |doi=10.5281/zenodo.8083652 |last16=Feulner |first16=Philine G D. |last17=Flouri |first17=Tomas |last18=Formenti |first18=Giulio |last19=Gissi |first19=Carmela |last20=Gregorič |first20=Matjaž |last21=Heinze |first21=Berthold |last22=Hindrikson |first22=Maris |last23=Höglund |first23=Jacob |last24=Hughes |first24=Graham M. |last25=Klinga |first25=Peter |last26=Kratochwil |first26=Claudius F. |last27=Kusza |first27=Szilvia |last28=Lucek |first28=Kay |last29=Magnússon |first29=Kristinn Pétur |last30=Manousaki |first30=Tereza}} Core Projects include the Pilot Project,{{Cite journal |last=Mc Cartney |first=Ann M. |last2=Formenti |first2=Giulio |last3=Mouton |first3=Alice |last4=De Panis |first4=Diego |last5=Marins |first5=Luísa S. |last6=Leitão |first6=Henrique G. |last7=Diedericks |first7=Genevieve |last8=Kirangwa |first8=Joseph |last9=Morselli |first9=Marco |last10=Salces-Ortiz |first10=Judit |last11=Escudero |first11=Nuria |last12=Iannucci |first12=Alessio |last13=Natali |first13=Chiara |last14=Svardal |first14=Hannes |last15=Fernández |first15=Rosa |date=2024-09-17 |title=The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics |url=https://www.nature.com/articles/s44185-024-00054-6 |journal=npj Biodiversity |language=en |volume=3 |issue=1 |pages=1–17 |doi=10.1038/s44185-024-00054-6 |issn=2731-4243|hdl=11585/986534 |hdl-access=free }} aiming to complete at least one reference genome from each ERGA-associated country, and the Horizon Europe funded Biodiversity Genomics Europe Project,{{Cite web |last=Genomics |first=Biodiversity |title=BGE Home |url=https://biodiversitygenomics.eu/ |access-date=2024-11-21 |website=Biodiversity Genomics Europe |language=en-GB}} a joint endeavour with the International Barcode of Life Europe community,{{Cite web |last=Europe |first=iBOL |title=iBOL Europe – European node of the International Barcode of Life |url=https://iboleurope.org/ |access-date=2024-11-21 |website=iBOL Europe |language=en-GB}} as well as building the ERGA Knowledge Hub{{Cite web |title=ERGA Knowledge Hub- Training material for Biodiversity Genomics |url=https://knowledge.erga-biodiversity.eu/ |access-date=2024-11-21 |website=knowledge.erga-biodiversity.eu |language=en}} that gathers and shares educational materials on biodiversity genomics and related topics to promote knowledge exchange.
References
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External links
- [https://www.erga-biodiversity.eu/ The European Reference Genome Atlas (ERGA)]