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Gouin A, Bretaudeau A, Nam K, Gimenez S, Aury JM, Duvic B, Hilliou F, Durand N, Montagné N, Darboux I, Kuwar S, Chertemps T, Siaussat D, Bretschneider A, Moné Y, Ahn SJ, Hänniger S, Grenet ASG, Neunemann D, Maumus F, Luyten I, Labadie K, Xu W, Koutroumpa F, Escoubas JM, Llopis A, Maïbèche-Coisne M, Salasc F, Tomar A, Anderson AR, Khan SA, Dumas P, Orsucci M, Guy J, Belser C, Alberti A, Noel B, Couloux A, Mercier J, Nidelet S, Dubois E, Liu NY, Boulogne I, Mirabeau O, Le Goff G, Gordon K, Oakeshott J, Consoli FL, Volkoff AN, Fescemyer HW, Marden JH, Luthe DS, Herrero S, Heckel DG, Wincker P, Kergoat GJ, Amselem J, Quesneville H, Groot AT, Jacquin-Joly E, Nègre N, Lemaitre C, Legeai F, d'Alençon E, Fournier P. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Sci Rep 2017; 7:11816. [PMID: 28947760 PMCID: PMC5613006 DOI: 10.1038/s41598-017-10461-4] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/19/2017] [Indexed: 12/30/2022] Open
Abstract
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
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Affiliation(s)
- Anaïs Gouin
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
| | - Anthony Bretaudeau
- INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), Campus Beaulieu, Rennes, 35042, France.,INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Kiwoong Nam
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Sylvie Gimenez
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Jean-Marc Aury
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Bernard Duvic
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Nicolas Durand
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Nicolas Montagné
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | | | - Suyog Kuwar
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Thomas Chertemps
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - David Siaussat
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Anne Bretschneider
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Yves Moné
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Sabine Hänniger
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | | | - David Neunemann
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Luyten
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Karine Labadie
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Wei Xu
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, 6150, Australia
| | - Fotini Koutroumpa
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France.,Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | | | - Angel Llopis
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain.,Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Martine Maïbèche-Coisne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Fanny Salasc
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.,EPHE, PSL Research University, UMR1333 - DGIMI, Pathologie comparée des Invertébrés CC101, F-34095, Montpellier cedex 5, France
| | - Archana Tomar
- Laboratory of Mammalian Genetics, Center for DNA Fingerprinting and Diagnostics (CDFD), Lab block: Tuljaguda (Opp. MJ Market), Nampally, Hyderabad, 500 001, India
| | - Alisha R Anderson
- CSIRO Ecosystem Sciences, Black Mountain, Canberra, ACT 2600, Australia
| | - Sher Afzal Khan
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | - Marion Orsucci
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France
| | - Julie Guy
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | | | - Benjamin Noel
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Arnaud Couloux
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France
| | | | - Sabine Nidelet
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Emeric Dubois
- Plateforme MGX, C/o institut de Génomique Fonctionnelle, 141, rue de la Cardonille, 34094, Montpellier cedex 05, France
| | - Nai-Yong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Isabelle Boulogne
- Sorbonne Universités, UPMC University Paris 06, Institute of Ecology and Environmental Sciences of Paris, 75005, Paris, France
| | - Olivier Mirabeau
- INRA, Institute of Ecology and Environmental Sciences, 78000, Versailles, France
| | - Gaelle Le Goff
- Université Côte d'Azur, INRA, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Karl Gordon
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - John Oakeshott
- CSIRO, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601, Australia
| | - Fernando L Consoli
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, Brazil
| | | | - Howard W Fescemyer
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - James H Marden
- Department of Biology, 208 Mueller Laboratory, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Dawn S Luthe
- Department of Plant Science, 102 Tyson Building, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
| | - Salvador Herrero
- Department of Genetics, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany
| | - Patrick Wincker
- CEA, Genoscope, 2 rue Gaston Crémieux, 91000, Evry, France.,CNRS UMR 8030, 2 rue Gaston Crémieux, 91000, Evry, France.,Université d'Evry Val D'Essonne, 91000, Evry, France
| | - Gael J Kergoat
- INRA, UMR1062 CBGP, IRD, CIRAD, Montpellier SupAgro, 755 Avenue du campus Agropolis, 34988, Montferrier/Lez, France
| | - Joelle Amselem
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Astrid T Groot
- Department of Entomology, Max Planck Institute for Chemical Ecology, D-07745, Jena, Germany.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Science Park 904, 1090 GE, Amsterdam, The Netherlands
| | | | - Nicolas Nègre
- DGIMI, INRA, Univ. Montpellier, 34095, Montpellier, France.
| | - Claire Lemaitre
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France.
| | - Fabrice Legeai
- INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes, 35042, France
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Arnoux E, Eraud C, Navarro N, Tougard C, Thomas A, Cavallo F, Vetter N, Faivre B, Garnier S. Morphology and genetics reveal an intriguing pattern of differentiation at a very small geographic scale in a bird species, the forest thrush Turdus lherminieri. Heredity (Edinb) 2014; 113:514-25. [PMID: 24984605 DOI: 10.1038/hdy.2014.56] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/11/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022] Open
Abstract
Mobile organisms are expected to show population differentiation only over fairly large geographical distances. However, there is growing evidence of discrepancy between dispersal potential and realized gene flow. Here we report an intriguing pattern of differentiation at a very small spatial scale in the forest thrush (Turdus lherminieri), a bird species endemic to the Lesser Antilles. Analysis of 331 individuals from 17 sampling sites distributed over three islands revealed a clear morphological and genetic differentiation between these islands isolated by 40-50 km. More surprisingly, we found that the phenotypic divergence between the two geographic zones of the island of Guadeloupe was associated with a very strong genetic differentiation (Fst from 0.073-0.153), making this pattern a remarkable case in birds given the very small spatial scale considered. Molecular data (mitochondrial control region sequences and microsatellite genotypes) suggest that this strong differentiation could have occurred in situ, although alternative hypotheses cannot be fully discarded. This study suggests that the ongoing habitat fragmentation, especially in tropical forests, may have a deeper impact than previously thought on avian populations.
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Affiliation(s)
- E Arnoux
- Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France
| | - C Eraud
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station Biologique de Chizé, Carrefour de la Canauderie, Villiers en Bois, France
| | - N Navarro
- 1] Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France [2] Laboratoire EPHE PALEVO-Ecole Pratique des Hautes Etudes, Dijon, France
| | - C Tougard
- Institut des Sciences de l'Evolution de Montpellier, IMR CNRS 5554 and UMR IRD 226, Université de Montpellier II, Place Eugène Bataillon, CC065, Montpellier, France
| | - A Thomas
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station Biologique de Chizé, Carrefour de la Canauderie, Villiers en Bois, France
| | - F Cavallo
- 1] Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France [2] Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station Biologique de Chizé, Carrefour de la Canauderie, Villiers en Bois, France
| | - N Vetter
- Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France
| | - B Faivre
- Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France
| | - S Garnier
- Biogéosciences, UMR CNRS 6282, Equipe BIOME, Université de Bourgogne, Dijon, France
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