Cited by 341Genomics and Phylogenetic StudiesGenetic diversity and population structureChromosomal and Genetic Variations

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The era of reference genomes in conservation genomics

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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., Pampoulie, Christophe, Ruiz-López, María J., Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Guojie, Mazzoni, Camila J., Jarvis, Erich D., Bálint, Miklós, Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle·2022·Trends in Ecology & Evolution

DOI 10.1016/j.tree.2021.11.008PMC PMC13065249

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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.

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Authors: Formenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Ciofi, C., Crottini, A., Godoy, J. A., Höglund, J., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Svardal, H., Theofanopoulou, C., de Vries, J., Waldvogel, A.-M., Zhang, G., Mazzoni, C. J., Jarvis, E. D., Bálint, M., Formenti, G., Theissinger, K., Fernandes, C., Bista, I., Bombarely, A., Bleidorn, C., Čiampor, F., Ciofi, C., Crottini, A., Godoy, J. A., Hoglund, J., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P., Pampoulie, C., Ruiz-López, M. J., Svardal, H., Theofanopoulou, C., de Vries, J., Waldvogel, A.-M., Zhang, G., Mazzoni, C. J., Jarvis, E., Bálint, M., Aghayan, S. A., Alioto, T. S., Almudi, I., Alvarez, N., Alves, P. C., Amorim, I. R., Antunes, A., Arribas, P., Baldrian, P., Berg, P. R., Bertorelle, G., Böhne, A., Bonisoli-Alquati, A., Boštjančić, L. L., Boussau, B., Breton, C. M., Buzan, E., Campos, P. F., Carreras, C., Castro, L. F., Chueca, L. J., Conti, E., Cook-Deegan, R., Croll, D., Cunha, M. V., Delsuc, F., Dennis, A. B., Dimitrov, D., Faria, R., Favre, A., Fedrigo, O. D., Fernández, R., Ficetola, G. F., Flot, J.-F., Gabaldón, T., Galea Agius, D. R., Gallo, G. R., Giani, A. M., Gilbert, M. T. P., Grebenc, T., Guschanski, K., Guyot, R., Hausdorf, B., Hawlitschek, O., Heintzman, P. D., Heinze, B., Hiller, M., Husemann, M., Iannucci, A., Irisarri, I., Jakobsen, K. S., Jentoft, S., Klinga, P., Kloch, A., Kratochwil, C. F., Kusche, H., Layton, K. K. S., Leonard, J. A., Lerat, E., Liti, G., Manousaki, T., Marques-Bonet, T., Matos-Maraví, P., Matschiner, M., Maumus, F., Mc Cartney, A. M., Meiri, S., Melo-Ferreira, J., Mengual, X., Monaghan, M. T., Montagna, M., Mysłajek, R. W., Neiber, M. T., Nicolas, V., Novo, M., Ozretić, P., Palero, F., Pârvulescu, L., Pascual, M., Paulo, O. S., Pavlek, M., Pegueroles, C., Pellissier, L., Pesole, G., Primmer, C. R., Riesgo, A., Rüber, L., Rubolini, D., Salvi, D., Seehausen, O., Seidel, M., Secomandi, S., Studer, B., Theodoridis, S., Thines, M., Urban, L., Vasemägi, A., Vella, A., Vella, N., Vernes, S. C., Vernesi, C., Vieites, D. R., Waterhouse, R. M., Wheat, C. W., Wörheide, G., Wurm, Y., & Zammit, G.
Affiliations: University of Copenhagen (DK)
Center for Coastal Studies (US)
University of Lisbon (PT)
Consejo Superior de Investigaciones Científicas (ES)
University of Liège (BE)
Laboratoire de Biométrie et Biologie Evolutive (FR)
Campus-Institut Data Science (CIDAS) (DE)
University of Cambridge (GB)
Rockefeller University (US)
ORCID: Zhang, Guojie
Čiampor, Fedor
Aghayan, Sargis A.
Alioto, Tyler S.
Alves, Paulo C.
Amorim, Isabel R.
Antunes, Agostinho
Arribas, Paula
Berg, Paul R.
Bertorelle, Giorgio
Böhne, Astrid
Boštjančić, Ljudevit L.
Boussau, Bastien
Breton, Catherine M.
Campos, Paula F.
Carreras, Carlos
Castro, L. FIlipe
Chueca, Luis J.
Conti, Elena
Cook-Deegan, Robert
Croll, Daniel
Cunha, Mónica V.
Delsuc, Frédéric
Dennis, Alice B.
Dimitrov, Dimitar
Faria, Rui
Favre, Adrien
Fedrigo, Olivier D.
Fernández, Rosa
Ficetola, Gentile Francesco
Flot, Jean-François
Gabaldón, Toni
Gallo, Guido R.
Giani, Alice M.
Gilbert, M. Thomas P.
Grebenc, Tine
Guschanski, Katerina
Guyot, Romain
Hausdorf, Bernhard
Hawlitschek, Oliver
Heintzman, Peter D.
Heinze, Berthold
Hiller, Michael
Husemann, Martin
Iannucci, Alessio
Irisarri, Iker
Jakobsen, Kjetill S.
Jentoft, Sissel
Klinga, Peter
Kloch, Agnieszka
Kratochwil, Claudius F.
Kusche, Henrik
Layton, Kara K.S.
Leonard, Jennifer A.
Lerat, Emmanuelle
Liti, Gianni
Manousaki, Tereza
Matschiner, Michael
Maumus, Florian
Meiri, Shai
Mengual, Ximo
Monaghan, Michael T.
Montagna, Matteo
Mysłajek, Robert W.
Neiber, Marco T.
Nicolas, Violaine
Novo, Marta
Ozretić, Petar
Palero, Ferran
Pârvulescu, Lucian
Pascual, Marta
Paulo, Octávio S.
Pavlek, Martina
Pegueroles, Cinta
Pellissier, Loïc
Pesole, Graziano
Primmer, Craig R.
Riesgo, Ana
Rüber, Lukas
Rubolini, Diego
Salvi, Daniele
Seidel, Matthias
Secomandi, Simona
Studer, Bruno
Theodoridis, Spyros
Thines, Marco
Urban, Lara
Vasemägi, Anti
Vella, Adriana
Vella, Noel
Vernes, Sonja C.
Vernesi, Cristiano
Vieites, David R.
Waterhouse, Robert M.
Wheat, Christopher W.
Wörheide, Gert
Wurm, Yannick
Zammit, Gabrielle
Venue: Trends in Ecology & Evolution
Publisher: Elsevier BV
Published: 2022-03
Volume: 37
Issue: 3
Pages: 197-202
ISSN: 0169-5347 (ISSN-L)
DOI: 10.1016/j.tree.2021.11.008
PMC: PMC13065249
OpenAlex: W4207054657
Cited by: 340
References: 14
Citations by year: 2026: 52 · 2025: 69 · 2024: 112 · 2023: 77 · 2022: 28
FWCI: 23.72
Type: journal article
Language: en
Open access: hybrid
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ETH Zürich Research Collection
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Funders: Howard Hughes Medical Institute
Arizona State University
Institute for Research in Biomedicine
Helsingin Yliopisto
University of Otago
Villum Fonden (00025900)
University of Bern
Queen Mary University of London
Università degli Studi di Milano
Institut de Recherche pour le Développement
Fondazione Edmund Mach
Universitat Pompeu Fabra
University of St Andrews
University of Edinburgh
University of Aberdeen
Institut National de la Santé et de la Recherche Médicale
Universidad Complutense de Madrid
Eidgenössische Technische Hochschule Zürich
Euskal Herriko Unibertsitatea
Institució Catalana de Recerca i Estudis Avançats
Universität Potsdam
Akademie Věd České Republiky
Sveriges Lantbruksuniversitet
Tel Aviv University
Università degli Studi di Firenze
Consiglio Nazionale delle Ricerche
Centre National de la Recherche Scientifique (UMR 5558)
Universitetet i Bergen
Université de Neuchâtel
Universitetet i Oslo
Ludwig-Maximilians-Universität München
Universidade de Lisboa
Universitat de Barcelona
Università degli Studi dell'Aquila
Université de Lausanne
Uniwersytet Warszawski
Universität Zürich
Universidade do Porto
Uppsala Universitet
Université Paris-Saclay
Institut Ruđer Bošković
Muséum National d'Histoire Naturelle
Freie Universität Berlin
Eesti Maaülikool
Université de Montpellier
Stockholms Universitet
Senckenberg Biodiversität und Klima Forschungszentrum
Université de Lyon
Swiss Federal Institute for Forest, Snow and Landscape Research
Centro Interdisciplinar de Investigação Marinha e Ambiental
Sorbonne Université
Nature
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
Max Planck Instituut voor Psycholinguïstiek
Directorate for Biological Sciences
Weill Cornell Medical College
Helsinki Institute of Life Science, Helsingin Yliopisto
Biotechnology and Biological Sciences Research Council (BB/T015683/1)
Leibniz-Gemeinschaft
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: reference genome, conservation genomics, genome sequencing, genomic diversity, population genomics, functional genomics, biodiversity, genome organization
MeSH terms: Genome, Genomics, Biodiversity

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The era of reference genomes in conservation genomics

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