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Singh KS, Cordeiro EMG, Troczka BJ, Pym A, Mackisack J, Mathers TC, Duarte A, Legeai F, Robin S, Bielza P, Burrack HJ, Charaabi K, Denholm I, Figueroa CC, ffrench-Constant RH, Jander G, Margaritopoulos JT, Mazzoni E, Nauen R, Ramírez CC, Ren G, Stepanyan I, Umina PA, Voronova NV, Vontas J, Williamson MS, Wilson ACC, Xi-Wu G, Youn YN, Zimmer CT, Simon JC, Hayward A, Bass C. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Commun Biol 2021; 4:847. [PMID: 34234279 PMCID: PMC8263593 DOI: 10.1038/s42003-021-02373-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host-plant associations, uncovering the widespread co-option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.
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Affiliation(s)
- Kumar Saurabh Singh
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Erick M. G. Cordeiro
- grid.11899.380000 0004 1937 0722Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz,”, Universidade de São Paulo, Piracicaba, Brazil
| | - Bartlomiej J. Troczka
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Adam Pym
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Joanna Mackisack
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Thomas C. Mathers
- grid.14830.3e0000 0001 2175 7246Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ana Duarte
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | | | | | - Pablo Bielza
- grid.218430.c0000 0001 2153 2602Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Hannah J. Burrack
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Kamel Charaabi
- Laboratory of Biotechnology and Nuclear Technologies, National Center of Nuclear Sciences and Technologies, Biotechpole of Sidi Thabet, Sidi Thabet, Ariana Tunisia
| | - Ian Denholm
- grid.5846.f0000 0001 2161 9644Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, UK
| | - Christian C. Figueroa
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Richard H. ffrench-Constant
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Georg Jander
- grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
| | - John T. Margaritopoulos
- Department of Plant Protection at Volos, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization ‘DEMETER’, Volos, Greece
| | - Emanuele Mazzoni
- grid.8142.f0000 0001 0941 3192Department of Sustainable Crop Production, Section Sustainable Crop and Food Protection, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ralf Nauen
- grid.420044.60000 0004 0374 4101Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Claudio C. Ramírez
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Guangwei Ren
- grid.410727.70000 0001 0526 1937Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ilona Stepanyan
- grid.418094.00000 0001 1146 7878Scientific Center of Zoology and Hydroecology, National Academy of Science, Republic of Armenia, Yerevan, Armenia
| | - Paul A. Umina
- Cesar, Parkville, Victoria Australia ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, Victoria Australia
| | - Nina V. Voronova
- grid.17678.3f0000 0001 1092 255XThe Department of General Ecology and Methods of Biology Teaching, Belarusian State University, Minsk, Republic of Belarus
| | - John Vontas
- grid.4834.b0000 0004 0635 685XInstitute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece ,grid.10985.350000 0001 0794 1186Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Martin S. Williamson
- grid.418374.d0000 0001 2227 9389Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Alex C. C. Wilson
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL USA
| | - Gao Xi-Wu
- grid.22935.3f0000 0004 0530 8290Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Young-Nam Youn
- grid.254230.20000 0001 0722 6377Department of Applied Biology, College of Agricultural and Life Science, Chungnam National University, Daejeon, Korea
| | - Christoph T. Zimmer
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK ,grid.420222.40000 0001 0669 0426Present Address: Syngenta Crop Protection, Werk Stein, Schaffhauserstrasse, Stein, Switzerland
| | | | - Alex Hayward
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Chris Bass
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
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Paril JF, Balding DJ, Fournier-Level A. Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations. Mol Ecol Resour 2021; 22:137-152. [PMID: 34192415 DOI: 10.1111/1755-0998.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 11/27/2022]
Abstract
Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.
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Affiliation(s)
- Jefferson F Paril
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - David J Balding
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandre Fournier-Level
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia
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Scanlan JL, Gledhill-Smith RS, Battlay P, Robin C. Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the 'detoxification-by-phosphorylation' enzymes of insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103429. [PMID: 32540344 DOI: 10.1016/j.ibmb.2020.103429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/25/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species of Drosophila and explored their evolution within the genus. Many ancestral EcKL clades are evolutionarily unstable and have experienced repeated gene gain and loss events, while others are conserved as single-copy orthologs. Leveraging multiple published gene expression datasets from D. melanogaster, and using the cytochrome P450s-a classical detoxification family-as a test case, we demonstrate relationships between xenobiotic induction, detoxification tissue-enriched expression and evolutionary instability in the EcKLs and the P450s. We devised a systematic method for identifying candidate detoxification genes in large gene families that is concordant with experimentally determined functions of P450 genes in D. melanogaster. Applying this method to the EcKLs suggested a significant proportion of these genes play roles in detoxification, and that the EcKLs may constitute a detoxification gene family in insects. Additionally, we estimate that between 11 and 16 uncharacterised D. melanogaster P450s are strong detoxification candidates. Lastly, we also found previously unreported genomic and transcriptomic variation in a number of EcKLs and P450s associated with toxic stress phenotypes using a targeted phenome-wide association study (PheWAS) approach in D. melanogaster, presenting multiple future avenues of research for detoxification genetics in this species.
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Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Rebecca S Gledhill-Smith
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Paul Battlay
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Parkville Campus, Melbourne, Victoria, 3010, Australia.
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Young HK, Denecke SM, Robin C, Fournier-Level A. Sublethal larval exposure to imidacloprid impacts adult behaviour in Drosophila melanogaster. J Evol Biol 2019; 33:151-164. [PMID: 31637792 DOI: 10.1111/jeb.13555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/27/2022]
Abstract
Pesticides are now chronically found in numerous ecosystems incurring widespread toxic effects on multiple organisms. For insects, the larvae are very exposed to pesticide pollution and the acute effect of insecticides on larvae has been characterized in a range of species. However, the carry-on effects in adults of sublethal exposure occurring in larvae are not well characterized. Here, we use a collection of strains of Drosophila melanogaster differing in their larval resistance to a commonly used insecticide, imidacloprid, and we test the effect of larval exposure on behavioural traits at the adult stage. Focusing on locomotor activity and on courtship and mating behaviour, we observed a significant carry-on effect of imidacloprid exposure. The heritability of activity traits measured in flies exposed to imidacloprid was higher than measured in controls and in these, courtship traits were genetically less correlated from mating success. Altogether, we did not observe a significant effect of the larval insecticide resistance status on adult behavioural traits, suggesting that selection for resistance in larvae does not involve repeatable behavioural changes in adults. This lack of correlation between larval resistance and adult behaviour also suggests that resistance at the larval stage does not necessarily result in increased behavioural resilience at a later life stage. These findings imply that selection for resistance in larvae as well as for behavioural resilience to sublethal exposure in adult will combine and impose a greater evolutionary constraint. Our conclusions further substantiate the need to encompass multiple trait measures and life stages in toxicological assays to properly assess the environmental impact of pesticides.
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Affiliation(s)
- Helen K Young
- School of BioSciences, The University of Melbourne, Parkville, Vic., Australia
| | - Shane M Denecke
- Institute of Molecular Biology and Biotechnology FORTH, Heraklion, Greece
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Parkville, Vic., Australia
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