[en] The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
Disciplines :
Biotechnology
Author, co-author :
Theissinger, Kathrin; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
Fernandes, Carlos; CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, 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
Formenti, Giulio; The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
Bista, Iliana; Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands, Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
Berg, Paul R; NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway, Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
Bleidorn, Christoph; University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
Bombarely, Aureliano; Universita degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
Crottini, Angelica; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal, BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
Gallo, Guido R; Department of Biosciences, University of Milan, Milan, Italy
Godoy, José A; Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
Jentoft, Sissel; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
Malukiewicz, Joanna; Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
Mouton, Alice ; Université de Liège - ULiège > Département des sciences et gestion de l'environnement (Arlon Campus Environnement) > Socio-économie, Environnement et Développement (SEED)
Oomen, Rebekah A; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
Paez, Sadye; The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
Palsbøll, Per J; 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
Pampoulie, Christophe; Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
Ruiz-López, María J; Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain, CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
Secomandi, Simona; Department of Biosciences, University of Milan, Milan, Italy
Svardal, Hannes; Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
Theofanopoulou, Constantina; The Rockefeller University, 1230 York Ave, New York, NY 10065, USA, Hunter College, City University of New York, NY, USA
de Vries, Jan; University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
Waldvogel, Ann-Marie; Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
Zhang, Guojie; Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China, Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
Jarvis, Erich D; The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
Bálint, Miklós; LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
Ciofi, Claudio; University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
Waterhouse, Robert M; University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Mazzoni, Camila J; 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
Höglund, Jacob; Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden. Electronic address: jacob.hoglund@ebc.uu.se
We thank Cecilia Helmerson, Antonio Rivas, Nelson Lauzon, and Sally Leys, for the pictures of the Atlantic cod, the Iberian lynx, the European beech, and the freshwater sponge, respectively. We also thank Fabien Condamine, Love Dalén, Richard Durbin, Bruno Fosso, Roderic Guigó, Marc Hanikenne, Alberto Pallavicini, Olga Vinnere Pettersson, Xavier Turon, and Detlef Weigel for their contributions to the manuscript, as well as the whole ERGA community for making this possible. No interests are declared.
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