doi: 10.1016/j.tree.2021.11.008.
Epub 2022 Jan 24.
The era of reference genomes in conservation genomics
Giulio Formenti
1
, Kathrin Theissinger
2
, Carlos Fernandes
3
, Iliana Bista
4
, Aureliano Bombarely
5
, Christoph Bleidorn
6
, Claudio Ciofi
7
, Angelica Crottini
8
, José A Godoy
9
, Jacob Höglund
10
, Joanna Malukiewicz
11
, Alice Mouton
12
, Rebekah A Oomen
13
, Sadye Paez
1
, Per J Palsbøll
14
, Christophe Pampoulie
15
, María J Ruiz-López
9
, Hannes Svardal
16
, Constantina Theofanopoulou
1
, Jan de Vries
17
, Ann-Marie Waldvogel
18
, Guojie Zhang
19
, Camila J Mazzoni
20
, Erich D Jarvis
1
, Miklós Bálint
21
; European Reference Genome Atlas (ERGA) Consortium
Collaborators,
Affiliations
Collaborators
-
European Reference Genome Atlas (ERGA) Consortium:
Giulio Formenti 22 , Kathrin Theissinger 23 , Carlos Fernandes 3 , Iliana Bista 24 , Aureliano Bombarely 25 , Christoph Bleidorn 26 , Fedor Čiampor 27 , Claudio Ciofi 7 , Angelica Crottini 28 , José A Godoy 29 , Jacob Hoglund 10 , Joanna Malukiewicz 30 , Alice Mouton 12 , Rebekah A Oomen 13 , Sadye Paez 22 , Per Palsbøll 31 , Christophe Pampoulie 32 , María José Ruiz-López 9 , Hannes Svardal 16 , Constantina Theofanopoulou 33 , Jan de Vries 34 , Ann-Marie Waldvogel 18 , Goujie Zhang 35 , Camila J Mazzoni 36 , Erich Jarvis 22 , Miklós Bálint 37 , Sargis A Aghayan 38 , Tyler S Alioto 39 , Isabel Almudi 40 , Nadir Alvarez 41 , Paulo C Alves 42 , Isabel R Amorim 43 , Agostinho Antunes 44 , Paula Arribas 45 , Petr Baldrian 46 , Paul R Berg 47 , Giorgio Bertorelle 48 , Astrid Böhne 49 , Andrea Bonisoli-Alquati 50 , Ljudevit L Boštjančić 51 , Bastien Boussau 52 , Catherine M Breton 53 , Elena Buzan 54 , Paula F Campos 55 , Carlos Carreras 40 , L FIlipe Castro 56 , Luis J Chueca 57 , Elena Conti 58 , Robert Cook-Deegan 59 , Daniel Croll 60 , Mónica V Cunha 61 , Frédéric Delsuc 62 , Alice B Dennis 63 , Dimitar Dimitrov 64 , Rui Faria 65 , Adrien Favre 66 , Olivier D Fedrigo 22 , Rosa Fernández 67 , Gentile Francesco Ficetola 68 , Jean-François Flot 69 , Toni Gabaldón 70 , Dolores R Galea Agius 71 , Guido R Gallo 72 , Alice M Giani 73 , M Thomas P Gilbert 74 , Tine Grebenc 75 , Katerina Guschanski 76 , Romain Guyot 77 , Bernhard Hausdorf 78 , Oliver Hawlitschek 78 , Peter D Heintzman 79 , Berthold Heinze 80 , Michael Hiller 81 , Martin Husemann 78 , Alessio Iannucci 7 , Iker Irisarri 82 , Kjetill S Jakobsen 83 , Sissel Jentoft 84 , Peter Klinga 85 , Agnieszka Kloch 86 , Claudius F Kratochwil 87 , Henrik Kusche 78 , Kara K S Layton 88 , Jennifer A Leonard 89 , Emmanuelle Lerat 90 , Gianni Liti 91 , Tereza Manousaki 92 , Tomas Marques-Bonet 93 , Pável Matos-Maraví 94 , Michael Matschiner 95 , Florian Maumus 96 , Ann M Mc Cartney 97 , Shai Meiri 98 , José Melo-Ferreira 99 , Ximo Mengual 100 , Michael T Monaghan 101 , Matteo Montagna 102 , Robert W Mysłajek 103 , Marco T Neiber 78 , Violaine Nicolas 104 , Marta Novo 105 , Petar Ozretić 106 , Ferran Palero 107 , Lucian Pârvulescu 108 , Marta Pascual 40 , Octávio S Paulo 109 , Martina Pavlek 110 , Cinta Pegueroles 40 , Loïc Pellissier 111 , Graziano Pesole 112 , Craig R Primmer 113 , Ana Riesgo 114 , Lukas Rüber 115 , Diego Rubolini 116 , Daniele Salvi 117 , Ole Seehausen 118 , Matthias Seidel 78 , Simona Secomandi 72 , Bruno Studer 119 , Spyros Theodoridis 120 , Marco Thines 121 , Lara Urban 122 , Anti Vasemägi 123 , Adriana Vella 124 , Noel Vella 125 , Sonja C Vernes 126 , Cristiano Vernesi 127 , David R Vieites 128 , Robert M Waterhouse 129 , Christopher W Wheat 130 , Gert Wörheide 131 , Yannick Wurm 132 , Gabrielle Zammit 133
Affiliations
- 1 The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
- 2 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 3 CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal.
- 4 University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK.
- 5 Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
- 6 University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany.
- 7 University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy.
- 8 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
- 9 Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain.
- 10 Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden.
- 11 German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.
- 12 InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium.
- 13 Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway.
- 14 Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA.
- 15 Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland.
- 16 Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium.
- 17 University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany.
- 18 Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany.
- 19 Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China.
- 20 Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany.
- 21 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. Electronic address: miklos.balint@senckenberg.de.
- 22 The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
- 23 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 24 University of Cambridge, Department of Genetics, Downing Street, CB2 3EH; Wellcome Sanger Institute, Hinxton, UK.
- 25 Universita degli Studi di Milano, Via Celoria 26, 20133, Italy.
- 26 University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073 Germany.
- 27 Plant Science and Biodiversity Centre, Slovak Academy of Science, Dúbravská cesta 9, 845 23 Bratislava, Slovakia.
- 28 CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal.
- 29 Estación Biológica de Doñana, Calle Americo Vespucio 26, 41092, Spain.
- 30 German Primate Center, Kellnerweg 4, 37077, Germany.
- 31 Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747 AG Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA.
- 32 Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland.
- 33 Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
- 34 University of Goettingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany.
- 35 Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Build 3, Universitetsparken 15, Copenhagen, 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Jiaochang East Road, Wupan District, Kunming, Yunnan 650223, China.
- 36 Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str, 17 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany.
- 37 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 38 Chair of Zoology, Yerevan State University, 1 Alex Manoogian, Yerevan, 0025, Armenia.
- 39 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
- 40 Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
- 41 Geneva Natural History Museum, 1 route de Malagnou, 1208 Geneva, Switzerland; University of Geneva, Department of Genetics & Evolution, University of Geneva, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland.
- 42 CIBIO/InBIO, University of Porto, Campus of Vairão, 4485-661, Vila do Conde, Portugal; Dep Biology, Faculty of Sciences, University of Porto, R Campo Alegre, s/n, 4169-007 Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA.
- 43 cE3c - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Universidade dos Açores, Rua Capitão João d'Àvila, Pico da Urze, 9700-042 Angra do Heroísmo, Azores, Portugal.
- 44 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
- 45 Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, 38206, Spain.
- 46 Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Praha 4 14220, Czech Republic.
- 47 University of Agder, Centre for Coastal Research, 25, Universitetsveien, Kristiansand N-4630, Norway; Norwegian Institute for Water Research (NIVA), 21, Gaustadallèen, Oslo N-0349, Norway.
- 48 Department of Life Sciences and Biotechnology, 46, via Borsari, Ferrara 44121, Italy.
- 49 Centre for Molecular Biodiversity Research, Zoological Reseach Museum Alexander Koenig Bonn, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
- 50 California State Polytechnic University, Pomona, 3801 W Temple Avenue, Pomona, CA 91767, USA.
- 51 LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 52 UMR5558, CNRS, Université Lyon 1, Université de Lyon, Bât. Grégor Mendel, 43 bd du 11 novembre 1918, Villeurbanne, France 69622.
- 53 Alliance Bioiversity CIAT, Europe - Montpellier Office, Bioversity International France, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France; French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France.
- 54 University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000 Koper, Slovenia; Environmental Protection College, Trg mladosti 7, 3320 Velenje, Slovenia.
- 55 CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos 4450-208, Portugal.
- 56 Interdisciplinary Centre of Marine and Environmental Research, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences University of Porto, Rua Campo Alegre s/n, Porto 4169-007, Portugal.
- 57 University of the Basque Country (UPV/EHU), 7, Paseo de la Universidad, Vitoria-Gasteiz 01006, Spain; LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), 25, Senckenberganlage, Frankfurt am Main 60325, Germany.
- 58 University of Zurich, Department of Systematic and Evolutionary Botany, 107 Zollikerstrasse, Zurich 8008, Switzerland.
- 59 Arizona State University, 1800 I (Eye) Street, NW, Washington, DC 20006, USA.
- 60 University of Neuchatel, 11, Emile-Argand, Neuchatel CH-2000, Switzerland.
- 61 Centre for Ecology, Evolution and Environmental Changes (CE3C), Campus da Faculdade de Ciências da Universidade de Lisboa, C2 Building, Campo Grande 1749-016, Lisboa, Portugal; BioISI- Biosystems and Integrative Sciences Institute, Campus da Faculdade de Ciências da Universidade de Lisboa, Teclabs Building, Campo Grande, 1749-016 Lisboa, Portugal.
- 62 Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France.
- 63 University of Potsdam, Institute for Biochemistry & Biology, Karl-Liebknecht-Str. 24-25, House 26, Room 2.77, 14476 Potsdam, Germany.
- 64 Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway.
- 65 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas N7, 4485-661 Vairão, Portugal.
- 66 Senckenberg Research Institute and Natural History Museum, 25 Senckenberganlage, Frankfurt/Main D-60325, Germany.
- 67 Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 37-49 Passeig marítim de la Barceloneta, Barcelona 08003, Spain.
- 68 Università degli Studi di Milano, Via Celoria 10, 20133 Milano, Italy; Univ. Grenoble-Alpes, F-38000 Grenoble, France.
- 69 Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium.
- 70 Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29., , 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
- 71 Centre of Molecular Medicine and Biobanking, Tal-Qroqq, Msida, MSD2080, Malta; Ġ.F. Abela Junior College, Department of Biology, Ġuzè Debono Square, Msida MSD 1252, Malta.
- 72 Department of Biosciences, University of Milan, Milan, Italy, 26, Via Celoria, Milan 20133, Italy.
- 73 Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA.
- 74 Center for Evolutionary Hologenomics, The GLOBE Institute, The University of Copenhagen, 5A, Oester Farimagsgade, Copenhagen, 1353, Denmark; University Museum, NTNU, 47B, Erling Skakkes gate, Trondheim, Norway.
- 75 Slovenian Forestry Institute, Večna pot 2, SI-1000 Ljubljana, Slovenia.
- 76 The University of Edinburgh, Institute of Evolutionary Biology, School of Biological Sciences, Ash worth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK; Uppsala University, Department of Ecology and Genetics/Animal Ecology, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
- 77 Institut de Recherche pour le Développement, 911, ave Agropolis, Montpellier, 34394, France.
- 78 Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.
- 79 The Arctic University Museum of Norway, UiT - The Arctic University of Norway, P.O. Box 6050, Langnes, Tromsø, N-9037, Norway.
- 80 Austrian Research Centre for Forests (BFW), 8, Seckendorff-Gudent Weg, Vienna, 1130, Austria.
- 81 LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany; Senckenberg Society for Nature Research, Senckenberganlage 25, 60325 Frankfurt, Germany; Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
- 82 University of Goettiingen, 1 Goldschmidtstr., Goettiingen, 37077, Germany; Campus Institute Data Science (CIDAS), Goettiingen, Germany.
- 83 Centre for Ecological and Evolutionary Synthesis (CEES), Dept. of Biosciences, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway.
- 84 University of Oslo, Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), Blindernveien 31, 0371 Oslo, Norway.
- 85 Technical University in Zvolen, Faculty of Forestry, Department of Phytology, 24, T.G. Masaryka, Zvolen, 960 01, Slovak Republic; DIANA - Carpathian Wildlife Research, 47, Mládežnícka, Banská Bystrica 974 04, Slovak Republic.
- 86 Institute of Functional Biology and Ecology, Department of Ecology, Univeristy of Warsaw, Faculty of Biology, Ilii, Miecznikowa 1, 02-096 Warszawa, Poland.
- 87 Institute of Biotechnology, HiLIFE, University of Helsinki, 1, Viikinkaari, Helsinki, 00790, Finland.
- 88 University of Aberdeen, Zoology Building, Tillydrone Ave, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- 89 Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio 26, Seville, 41092, Spain.
- 90 Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France.
- 91 Université Côte d'Azur, CNRS, INSERM, IRCAN, 28 Avenue de Valombrose, 06107 NICE Cedex 2, France.
- 92 Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.
- 93 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
- 94 Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.
- 95 University of Oslo, 1, Sars' gate, Oslo, 0562, Norway.
- 96 Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France.
- 97 National Institute of Health, 49 Convent Drive, Bethesda, MD 20892, USA.
- 98 Tel Aviv University, School of Zoology, the Steinhardt Museum of Natural History, 12 Klausner street, Tel Aviv 6997801, Israel.
- 99 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 7, Rua Padre Armando Quintas, Vairão, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, s/n, Rua do Campo Alegre, Porto 4169-007, Portugal.
- 100 Centre of Taxonomy and Evolutionary Research, Zoological Reseach Museum Alexander Koenig Bonn, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
- 101 Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 301, Müggelseedamm, Berlin, 12587, Germany; Institut für Biologie, Freie Universität Berlin, 1-3, Königin-Luise-Str., Berlin 12489, Germany.
- 102 Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, 2, Via Celoria, Milan, I-20133, Italy; BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 100, Via Università, Portici I-80055, Italy.
- 103 University of Warsaw, Faculty of Biology, Institute of Functional Biology and Ecology, Department of Ecology, Biological and Chemical Research Centre, 101 Zwirki i Wigury, Warszawa, 02-089, Poland.
- 104 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France.
- 105 Complutense University of Madrid, José Antonio Nováis, 12, Madrid, 28040, Spain.
- 106 Ruđer Bošković Institute, 54, Bijenička Road, Zagreb, HR-10000, Croatia.
- 107 Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de Valencia, Carrer del Catedrátic José Beltrán Martinez 2, 46980 Paterna, Spain.
- 108 Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, 16A Pestalozzi St., Timisoara, 300115, Romania; Environmental Advanced Research Institute, West University of Timisoara, Vasile Pârvan 4 Bd., Timisoara 300223, Romania.
- 109 cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, P-1749-016, Lisboa.
- 110 Ruder Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia; Croatian Biospeleological Society, Rooseveltov trg 6, Zagreb 10000, Croatia.
- 111 ETH Zürich, Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland; Swiss Federal Institute for Forest Snow and Landscape Research WSL, Unit of Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.
- 112 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Campus "E. Quagliariello", voa Orabona, 4, 70126 Bari, Italy; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Campus "E. Quagliariello", voa Orabona, 4, 70126 Bari, Italy; Consorzio Interuniversitario Bioteconologie, via Flavia, 23/1, 34148 Trieste, Italy.
- 113 Organismal and Evolutionary Biology Research Program, University of Helsinki, PO Box 56, 00014, University of Helsinki, Finland; Institute of Biotechnology (HiLIFE), University of Helsinki, PO Box 56, 00014, Finland.
- 114 Museo Nacional de Ciencias Naturales - CSIC, C/ José Gutiérrez Abascal, 2, Madrid, 28028, Spain; Natural History Museum of London, Cromwell Road, SW7 5BD London, UK.
- 115 Naturhistorisches Museum Bern, 15 Bernastrasse, Bern, 3005, Switzerland; Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 6 Balzerstrasse, Bern 3012, Switzerland.
- 116 Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 26, Milano, I-20133, Italy.
- 117 Department of Health, Life & Environmental Sciences - University of L'Aquila, Via Vetoio snc, 67100 L'Aquila-Coppito, Italy.
- 118 Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Federal Institute for Aquatic Science & Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.
- 119 Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland.
- 120 Senckenberg Biodiversität und Klima Forschungszentrum: Frankfurt, DE, 25 Senckenberganlage, Frankfurt am Main 60325, Germany.
- 121 Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany; Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main 60325, Germany; LOEWE Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, Frankfurt am Main 60325, Germany.
- 122 Department of Anatomy, University of Otago, 270 Gt King Street, Dunedin, 9016, New Zealand.
- 123 Department of Aquatic Resources, Swedish University of Agricultural Sciences, 2, Stångholmsvägen, Drottningholm, 178 93, Sweden; Chair of Aquaculture, Institute of Veterinary Medicine and Animal, Estonian Uiversity of Life Sciences, 56A, Kreutzwaldi, Tartu 51006, Estonia.
- 124 Conservation Biology Research Group, University of Malta, Taq-Qroqq, Msida, MSD2080, Malta.
- 125 Conservation Biology Research Group, University of Malta, Msida, MSD2080, Malta.
- 126 School of Biology, The University of St Andrews, St Andrews, Fife, UK; Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, the Netherlands.
- 127 Forest Ecology and Biogeochemical Fluxes Unit, Research and Innovation Centre-Fondazione Edmund Mach, 1, via Edmund Mach, San Michele all'Adige, 38010, Italy.
- 128 Museo Nacional de Ciencias Naturales -CSIC, Calle José Gutierrez Abascal 2, 28006, Madrid, Spain.
- 129 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
- 130 Department of Zoology, Stockholm University, 18B, Svante Arrheniusväg, Stockholm, S-10691, Sweden.
- 131 Ludwig-Maximilians-Universität München, Dept. of Earth and Environmental Sciences, Paleontology & Geobiology, Richard-Wagner-Str. 10, Munich, 80333, Germany; Ludwig-Maximilians-Universität München, GeoBio-Center, Richard-Wagner-Str. 10, Munich 80333, Germany; SNSB - Bavarian State Collections for Palaeontology and Geology, Richard-Wagner-Str. 10, Munich 80333, Germany.
- 132 Queen Mary University of London, Mile End Road, London, E5 8HS, United Kingdom; Alan Turing Institute, London NW1 2DB, UK.
- 133 Department of Biology, University of Malta, Biomedical Sciences Building, MSD2080, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, MSD2080 Msida, Malta.
- PMID: 35086739
- DOI: 10.1016/j.tree.2021.11.008
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The era of reference genomes in conservation genomics
Giulio Formenti et al.
Trends Ecol Evol.
2022 Mar.
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doi: 10.1016/j.tree.2021.11.008.
Epub 2022 Jan 24.
Authors
Giulio Formenti
1
, Kathrin Theissinger
2
, Carlos Fernandes
3
, Iliana Bista
4
, Aureliano Bombarely
5
, Christoph Bleidorn
6
, Claudio Ciofi
7
, Angelica Crottini
8
, José A Godoy
9
, Jacob Höglund
10
, Joanna Malukiewicz
11
, Alice Mouton
12
, Rebekah A Oomen
13
, Sadye Paez
1
, Per J Palsbøll
14
, Christophe Pampoulie
15
, María J Ruiz-López
9
, Hannes Svardal
16
, Constantina Theofanopoulou
1
, Jan de Vries
17
, Ann-Marie Waldvogel
18
, Guojie Zhang
19
, Camila J Mazzoni
20
, Erich D Jarvis
1
, Miklós Bálint
21
; European Reference Genome Atlas (ERGA) Consortium
Collaborators
-
European Reference Genome Atlas (ERGA) Consortium:
Giulio Formenti 22 , Kathrin Theissinger 23 , Carlos Fernandes 3 , Iliana Bista 24 , Aureliano Bombarely 25 , Christoph Bleidorn 26 , Fedor Čiampor 27 , Claudio Ciofi 7 , Angelica Crottini 28 , José A Godoy 29 , Jacob Hoglund 10 , Joanna Malukiewicz 30 , Alice Mouton 12 , Rebekah A Oomen 13 , Sadye Paez 22 , Per Palsbøll 31 , Christophe Pampoulie 32 , María José Ruiz-López 9 , Hannes Svardal 16 , Constantina Theofanopoulou 33 , Jan de Vries 34 , Ann-Marie Waldvogel 18 , Goujie Zhang 35 , Camila J Mazzoni 36 , Erich Jarvis 22 , Miklós Bálint 37 , Sargis A Aghayan 38 , Tyler S Alioto 39 , Isabel Almudi 40 , Nadir Alvarez 41 , Paulo C Alves 42 , Isabel R Amorim 43 , Agostinho Antunes 44 , Paula Arribas 45 , Petr Baldrian 46 , Paul R Berg 47 , Giorgio Bertorelle 48 , Astrid Böhne 49 , Andrea Bonisoli-Alquati 50 , Ljudevit L Boštjančić 51 , Bastien Boussau 52 , Catherine M Breton 53 , Elena Buzan 54 , Paula F Campos 55 , Carlos Carreras 40 , L FIlipe Castro 56 , Luis J Chueca 57 , Elena Conti 58 , Robert Cook-Deegan 59 , Daniel Croll 60 , Mónica V Cunha 61 , Frédéric Delsuc 62 , Alice B Dennis 63 , Dimitar Dimitrov 64 , Rui Faria 65 , Adrien Favre 66 , Olivier D Fedrigo 22 , Rosa Fernández 67 , Gentile Francesco Ficetola 68 , Jean-François Flot 69 , Toni Gabaldón 70 , Dolores R Galea Agius 71 , Guido R Gallo 72 , Alice M Giani 73 , M Thomas P Gilbert 74 , Tine Grebenc 75 , Katerina Guschanski 76 , Romain Guyot 77 , Bernhard Hausdorf 78 , Oliver Hawlitschek 78 , Peter D Heintzman 79 , Berthold Heinze 80 , Michael Hiller 81 , Martin Husemann 78 , Alessio Iannucci 7 , Iker Irisarri 82 , Kjetill S Jakobsen 83 , Sissel Jentoft 84 , Peter Klinga 85 , Agnieszka Kloch 86 , Claudius F Kratochwil 87 , Henrik Kusche 78 , Kara K S Layton 88 , Jennifer A Leonard 89 , Emmanuelle Lerat 90 , Gianni Liti 91 , Tereza Manousaki 92 , Tomas Marques-Bonet 93 , Pável Matos-Maraví 94 , Michael Matschiner 95 , Florian Maumus 96 , Ann M Mc Cartney 97 , Shai Meiri 98 , José Melo-Ferreira 99 , Ximo Mengual 100 , Michael T Monaghan 101 , Matteo Montagna 102 , Robert W Mysłajek 103 , Marco T Neiber 78 , Violaine Nicolas 104 , Marta Novo 105 , Petar Ozretić 106 , Ferran Palero 107 , Lucian Pârvulescu 108 , Marta Pascual 40 , Octávio S Paulo 109 , Martina Pavlek 110 , Cinta Pegueroles 40 , Loïc Pellissier 111 , Graziano Pesole 112 , Craig R Primmer 113 , Ana Riesgo 114 , Lukas Rüber 115 , Diego Rubolini 116 , Daniele Salvi 117 , Ole Seehausen 118 , Matthias Seidel 78 , Simona Secomandi 72 , Bruno Studer 119 , Spyros Theodoridis 120 , Marco Thines 121 , Lara Urban 122 , Anti Vasemägi 123 , Adriana Vella 124 , Noel Vella 125 , Sonja C Vernes 126 , Cristiano Vernesi 127 , David R Vieites 128 , Robert M Waterhouse 129 , Christopher W Wheat 130 , Gert Wörheide 131 , Yannick Wurm 132 , Gabrielle Zammit 133
Affiliations
- 1 The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
- 2 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 3 CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal.
- 4 University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK.
- 5 Universita degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
- 6 University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany.
- 7 University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy.
- 8 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
- 9 Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain.
- 10 Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden.
- 11 German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.
- 12 InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium.
- 13 Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway.
- 14 Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA.
- 15 Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland.
- 16 Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium.
- 17 University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany.
- 18 Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany.
- 19 Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China.
- 20 Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany.
- 21 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. Electronic address: miklos.balint@senckenberg.de.
- 22 The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
- 23 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 24 University of Cambridge, Department of Genetics, Downing Street, CB2 3EH; Wellcome Sanger Institute, Hinxton, UK.
- 25 Universita degli Studi di Milano, Via Celoria 26, 20133, Italy.
- 26 University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073 Germany.
- 27 Plant Science and Biodiversity Centre, Slovak Academy of Science, Dúbravská cesta 9, 845 23 Bratislava, Slovakia.
- 28 CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal.
- 29 Estación Biológica de Doñana, Calle Americo Vespucio 26, 41092, Spain.
- 30 German Primate Center, Kellnerweg 4, 37077, Germany.
- 31 Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747 AG Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA.
- 32 Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland.
- 33 Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
- 34 University of Goettingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany.
- 35 Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Build 3, Universitetsparken 15, Copenhagen, 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Jiaochang East Road, Wupan District, Kunming, Yunnan 650223, China.
- 36 Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str, 17 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany.
- 37 LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 38 Chair of Zoology, Yerevan State University, 1 Alex Manoogian, Yerevan, 0025, Armenia.
- 39 CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
- 40 Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
- 41 Geneva Natural History Museum, 1 route de Malagnou, 1208 Geneva, Switzerland; University of Geneva, Department of Genetics & Evolution, University of Geneva, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland.
- 42 CIBIO/InBIO, University of Porto, Campus of Vairão, 4485-661, Vila do Conde, Portugal; Dep Biology, Faculty of Sciences, University of Porto, R Campo Alegre, s/n, 4169-007 Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA.
- 43 cE3c - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Universidade dos Açores, Rua Capitão João d'Àvila, Pico da Urze, 9700-042 Angra do Heroísmo, Azores, Portugal.
- 44 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
- 45 Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, 38206, Spain.
- 46 Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Praha 4 14220, Czech Republic.
- 47 University of Agder, Centre for Coastal Research, 25, Universitetsveien, Kristiansand N-4630, Norway; Norwegian Institute for Water Research (NIVA), 21, Gaustadallèen, Oslo N-0349, Norway.
- 48 Department of Life Sciences and Biotechnology, 46, via Borsari, Ferrara 44121, Italy.
- 49 Centre for Molecular Biodiversity Research, Zoological Reseach Museum Alexander Koenig Bonn, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
- 50 California State Polytechnic University, Pomona, 3801 W Temple Avenue, Pomona, CA 91767, USA.
- 51 LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany.
- 52 UMR5558, CNRS, Université Lyon 1, Université de Lyon, Bât. Grégor Mendel, 43 bd du 11 novembre 1918, Villeurbanne, France 69622.
- 53 Alliance Bioiversity CIAT, Europe - Montpellier Office, Bioversity International France, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France; French Institute of Bioinformatics (IFB)-South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France.
- 54 University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000 Koper, Slovenia; Environmental Protection College, Trg mladosti 7, 3320 Velenje, Slovenia.
- 55 CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, Matosinhos 4450-208, Portugal.
- 56 Interdisciplinary Centre of Marine and Environmental Research, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences University of Porto, Rua Campo Alegre s/n, Porto 4169-007, Portugal.
- 57 University of the Basque Country (UPV/EHU), 7, Paseo de la Universidad, Vitoria-Gasteiz 01006, Spain; LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), 25, Senckenberganlage, Frankfurt am Main 60325, Germany.
- 58 University of Zurich, Department of Systematic and Evolutionary Botany, 107 Zollikerstrasse, Zurich 8008, Switzerland.
- 59 Arizona State University, 1800 I (Eye) Street, NW, Washington, DC 20006, USA.
- 60 University of Neuchatel, 11, Emile-Argand, Neuchatel CH-2000, Switzerland.
- 61 Centre for Ecology, Evolution and Environmental Changes (CE3C), Campus da Faculdade de Ciências da Universidade de Lisboa, C2 Building, Campo Grande 1749-016, Lisboa, Portugal; BioISI- Biosystems and Integrative Sciences Institute, Campus da Faculdade de Ciências da Universidade de Lisboa, Teclabs Building, Campo Grande, 1749-016 Lisboa, Portugal.
- 62 Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France.
- 63 University of Potsdam, Institute for Biochemistry & Biology, Karl-Liebknecht-Str. 24-25, House 26, Room 2.77, 14476 Potsdam, Germany.
- 64 Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway.
- 65 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos; InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas N7, 4485-661 Vairão, Portugal.
- 66 Senckenberg Research Institute and Natural History Museum, 25 Senckenberganlage, Frankfurt/Main D-60325, Germany.
- 67 Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 37-49 Passeig marítim de la Barceloneta, Barcelona 08003, Spain.
- 68 Università degli Studi di Milano, Via Celoria 10, 20133 Milano, Italy; Univ. Grenoble-Alpes, F-38000 Grenoble, France.
- 69 Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium.
- 70 Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29., , 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB), Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
- 71 Centre of Molecular Medicine and Biobanking, Tal-Qroqq, Msida, MSD2080, Malta; Ġ.F. Abela Junior College, Department of Biology, Ġuzè Debono Square, Msida MSD 1252, Malta.
- 72 Department of Biosciences, University of Milan, Milan, Italy, 26, Via Celoria, Milan 20133, Italy.
- 73 Weill Cornell Medicine, 1300 York Ave, New York, NY 10065, USA.
- 74 Center for Evolutionary Hologenomics, The GLOBE Institute, The University of Copenhagen, 5A, Oester Farimagsgade, Copenhagen, 1353, Denmark; University Museum, NTNU, 47B, Erling Skakkes gate, Trondheim, Norway.
- 75 Slovenian Forestry Institute, Večna pot 2, SI-1000 Ljubljana, Slovenia.
- 76 The University of Edinburgh, Institute of Evolutionary Biology, School of Biological Sciences, Ash worth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK; Uppsala University, Department of Ecology and Genetics/Animal Ecology, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
- 77 Institut de Recherche pour le Développement, 911, ave Agropolis, Montpellier, 34394, France.
- 78 Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.
- 79 The Arctic University Museum of Norway, UiT - The Arctic University of Norway, P.O. Box 6050, Langnes, Tromsø, N-9037, Norway.
- 80 Austrian Research Centre for Forests (BFW), 8, Seckendorff-Gudent Weg, Vienna, 1130, Austria.
- 81 LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany; Senckenberg Society for Nature Research, Senckenberganlage 25, 60325 Frankfurt, Germany; Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
- 82 University of Goettiingen, 1 Goldschmidtstr., Goettiingen, 37077, Germany; Campus Institute Data Science (CIDAS), Goettiingen, Germany.
- 83 Centre for Ecological and Evolutionary Synthesis (CEES), Dept. of Biosciences, University of Oslo, PO Box 1066, Blindern, NO-0316 Oslo, Norway.
- 84 University of Oslo, Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), Blindernveien 31, 0371 Oslo, Norway.
- 85 Technical University in Zvolen, Faculty of Forestry, Department of Phytology, 24, T.G. Masaryka, Zvolen, 960 01, Slovak Republic; DIANA - Carpathian Wildlife Research, 47, Mládežnícka, Banská Bystrica 974 04, Slovak Republic.
- 86 Institute of Functional Biology and Ecology, Department of Ecology, Univeristy of Warsaw, Faculty of Biology, Ilii, Miecznikowa 1, 02-096 Warszawa, Poland.
- 87 Institute of Biotechnology, HiLIFE, University of Helsinki, 1, Viikinkaari, Helsinki, 00790, Finland.
- 88 University of Aberdeen, Zoology Building, Tillydrone Ave, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
- 89 Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio 26, Seville, 41092, Spain.
- 90 Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France.
- 91 Université Côte d'Azur, CNRS, INSERM, IRCAN, 28 Avenue de Valombrose, 06107 NICE Cedex 2, France.
- 92 Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Former U.S. Base of Gournes, P.O. Box 2214, 71003, Heraklion, Crete, Greece.
- 93 Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
- 94 Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.
- 95 University of Oslo, 1, Sars' gate, Oslo, 0562, Norway.
- 96 Université Paris-Saclay, INRAE, URGI, 78026, Versailles, France.
- 97 National Institute of Health, 49 Convent Drive, Bethesda, MD 20892, USA.
- 98 Tel Aviv University, School of Zoology, the Steinhardt Museum of Natural History, 12 Klausner street, Tel Aviv 6997801, Israel.
- 99 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 7, Rua Padre Armando Quintas, Vairão, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, s/n, Rua do Campo Alegre, Porto 4169-007, Portugal.
- 100 Centre of Taxonomy and Evolutionary Research, Zoological Reseach Museum Alexander Koenig Bonn, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany.
- 101 Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 301, Müggelseedamm, Berlin, 12587, Germany; Institut für Biologie, Freie Universität Berlin, 1-3, Königin-Luise-Str., Berlin 12489, Germany.
- 102 Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, 2, Via Celoria, Milan, I-20133, Italy; BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 100, Via Università, Portici I-80055, Italy.
- 103 University of Warsaw, Faculty of Biology, Institute of Functional Biology and Ecology, Department of Ecology, Biological and Chemical Research Centre, 101 Zwirki i Wigury, Warszawa, 02-089, Poland.
- 104 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France.
- 105 Complutense University of Madrid, José Antonio Nováis, 12, Madrid, 28040, Spain.
- 106 Ruđer Bošković Institute, 54, Bijenička Road, Zagreb, HR-10000, Croatia.
- 107 Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de Valencia, Carrer del Catedrátic José Beltrán Martinez 2, 46980 Paterna, Spain.
- 108 Department of Biology-Chemistry, Faculty of Chemistry, Biology, Geography, West University of Timisoara, 16A Pestalozzi St., Timisoara, 300115, Romania; Environmental Advanced Research Institute, West University of Timisoara, Vasile Pârvan 4 Bd., Timisoara 300223, Romania.
- 109 cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, P-1749-016, Lisboa.
- 110 Ruder Boskovic Institute, Bijenicka 54, Zagreb, 10000, Croatia; Croatian Biospeleological Society, Rooseveltov trg 6, Zagreb 10000, Croatia.
- 111 ETH Zürich, Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland; Swiss Federal Institute for Forest Snow and Landscape Research WSL, Unit of Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland.
- 112 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro", Campus "E. Quagliariello", voa Orabona, 4, 70126 Bari, Italy; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Campus "E. Quagliariello", voa Orabona, 4, 70126 Bari, Italy; Consorzio Interuniversitario Bioteconologie, via Flavia, 23/1, 34148 Trieste, Italy.
- 113 Organismal and Evolutionary Biology Research Program, University of Helsinki, PO Box 56, 00014, University of Helsinki, Finland; Institute of Biotechnology (HiLIFE), University of Helsinki, PO Box 56, 00014, Finland.
- 114 Museo Nacional de Ciencias Naturales - CSIC, C/ José Gutiérrez Abascal, 2, Madrid, 28028, Spain; Natural History Museum of London, Cromwell Road, SW7 5BD London, UK.
- 115 Naturhistorisches Museum Bern, 15 Bernastrasse, Bern, 3005, Switzerland; Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 6 Balzerstrasse, Bern 3012, Switzerland.
- 116 Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 26, Milano, I-20133, Italy.
- 117 Department of Health, Life & Environmental Sciences - University of L'Aquila, Via Vetoio snc, 67100 L'Aquila-Coppito, Italy.
- 118 Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland; Swiss Federal Institute for Aquatic Science & Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.
- 119 Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092 Zurich, Switzerland.
- 120 Senckenberg Biodiversität und Klima Forschungszentrum: Frankfurt, DE, 25 Senckenberganlage, Frankfurt am Main 60325, Germany.
- 121 Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany; Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, Frankfurt am Main 60325, Germany; LOEWE Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, Frankfurt am Main 60325, Germany.
- 122 Department of Anatomy, University of Otago, 270 Gt King Street, Dunedin, 9016, New Zealand.
- 123 Department of Aquatic Resources, Swedish University of Agricultural Sciences, 2, Stångholmsvägen, Drottningholm, 178 93, Sweden; Chair of Aquaculture, Institute of Veterinary Medicine and Animal, Estonian Uiversity of Life Sciences, 56A, Kreutzwaldi, Tartu 51006, Estonia.
- 124 Conservation Biology Research Group, University of Malta, Taq-Qroqq, Msida, MSD2080, Malta.
- 125 Conservation Biology Research Group, University of Malta, Msida, MSD2080, Malta.
- 126 School of Biology, The University of St Andrews, St Andrews, Fife, UK; Max Planck Institute for Psycholinguistics, Wundtlaan 1, Nijmegen, the Netherlands.
- 127 Forest Ecology and Biogeochemical Fluxes Unit, Research and Innovation Centre-Fondazione Edmund Mach, 1, via Edmund Mach, San Michele all'Adige, 38010, Italy.
- 128 Museo Nacional de Ciencias Naturales -CSIC, Calle José Gutierrez Abascal 2, 28006, Madrid, Spain.
- 129 Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
- 130 Department of Zoology, Stockholm University, 18B, Svante Arrheniusväg, Stockholm, S-10691, Sweden.
- 131 Ludwig-Maximilians-Universität München, Dept. of Earth and Environmental Sciences, Paleontology & Geobiology, Richard-Wagner-Str. 10, Munich, 80333, Germany; Ludwig-Maximilians-Universität München, GeoBio-Center, Richard-Wagner-Str. 10, Munich 80333, Germany; SNSB - Bavarian State Collections for Palaeontology and Geology, Richard-Wagner-Str. 10, Munich 80333, Germany.
- 132 Queen Mary University of London, Mile End Road, London, E5 8HS, United Kingdom; Alan Turing Institute, London NW1 2DB, UK.
- 133 Department of Biology, University of Malta, Biomedical Sciences Building, MSD2080, Msida, Malta; Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, MSD2080 Msida, Malta.
- PMID: 35086739
- DOI: 10.1016/j.tree.2021.11.008
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Abstract
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Keywords: ERGA; European Reference Genome Atlas; biodiversity conservation; conservation genetics.
Copyright © 2021. Published by Elsevier Ltd.
Conflict of interest statement
Declaration of interests The authors declare no conflicts of interest.
