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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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Ulrich GF, Zemp N, Vorburger C, Boulain H. Quantitative trait locus analysis of parasitoid counteradaptation to symbiont-conferred resistance. Heredity (Edinb) 2021; 127:219-232. [PMID: 34012059 PMCID: PMC8322320 DOI: 10.1038/s41437-021-00444-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 02/04/2023] Open
Abstract
Insect hosts and parasitoids are engaged in an intense struggle of antagonistic coevolution. Infection with heritable bacterial endosymbionts can substantially increase the resistance of aphids to parasitoid wasps, which exerts selection on parasitoids to overcome this symbiont-conferred protection (counteradaptation). Experimental evolution in the laboratory has produced counteradapted populations of the parasitoid wasp Lysiphlebus fabarum. These populations can parasitize black bean aphids (Aphis fabae) protected by the bacterial endosymbiont Hamiltonella defensa, which confers high resistance against L. fabarum. We used two experimentally evolved parasitoid populations to study the genetic architecture of the counteradaptation to symbiont-conferred resistance by QTL analysis. With simple crossing experiments, we showed that the counteradaptation is a recessive trait depending on the maternal genotype. Based on these results, we designed a customized crossing scheme to genotype a mapping population phenotyped for the ability to parasitize Hamiltonella-protected aphids. Using 1835 SNP markers obtained by ddRAD sequencing, we constructed a high-density linkage map consisting of six linkage groups (LGs) with an overall length of 828.3 cM and an average marker spacing of 0.45 cM. We identified a single QTL associated with the counteradaptation to Hamiltonella in L. fabarum on linkage group 2. Out of 120 genes located in this QTL, several genes encoding putative venoms may represent candidates for counteradaptation, as parasitoid wasps inject venoms into their hosts during oviposition.
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Affiliation(s)
- Gabriel F. Ulrich
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre, Department of Environmental Systems Sciences, ETH Zürich, 8092 Zürich, Switzerland
| | - Christoph Vorburger
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.5801.c0000 0001 2156 2780Institute of Integrative Biology, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Hélène Boulain
- grid.418656.80000 0001 1551 0562EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland ,grid.9851.50000 0001 2165 4204Present Address: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny. G3-GENES GENOMES GENETICS 2020; 10:4115-4128. [PMID: 32912931 PMCID: PMC7642942 DOI: 10.1534/g3.120.401485] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.
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Sugimoto N, Takahashi A, Ihara R, Itoh Y, Jouraku A, Van Leeuwen T, Osakabe M. QTL mapping using microsatellite linkage reveals target-site mutations associated with high levels of resistance against three mitochondrial complex II inhibitors in Tetranychus urticae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:103410. [PMID: 32442626 DOI: 10.1016/j.ibmb.2020.103410] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/28/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
The acaricides cyflumetofen, cyenopyrafen, and pyflubumide act as inhibitors of the mitochondrial electron transport system at complex II (succinate dehydrogenase; SDH), a new mode of action in arthropods. The development and mechanisms of low-level resistance against cyenopyrafen and cyflumetofen have been previously reported in Tetranychus urticae. In the present study, we investigated high levels of resistance against three SDH inhibitors in T. urticae field populations and clarify the genetic basis of resistance using quantitative trait locus (QTL) analysis. First, we constructed a microsatellite linkage map comprising 64 markers assembled into three linkage groups (LGs) with total length of 683.8 cM and average marker spacing of 11.03 cM. We then used the linkage map to perform QTL mapping, and identified significant QTLs contributing to resistance to cyflumetofen (one QTL on LG1), cyenopyrafen (one QTL on LG3), and pyflubumide (two QTLs on LG1 and LG3). The QTL peaks on LG1 for cyflumetofen and pyflubumide overlapped and included the SdhB locus. For cyenopyrafen resistance, the QTLs on LG3 included the SdhC locus. For cyflumetofen resistance, we found an I260T mutation in SdhB. For pyflubumide and cyenopyrafen resistance, we detected I260V and S56L substitutions in SdhB and SdhC, respectively, by direct sequencing. Both I260 in SdhB and S56 in SdhC were present in highly conserved regions of the ubiquinone binding site formed at the interface among SdhB, SdhC, and SdhD. Mutations at these positions have been implicated in resistance against fungicides that act as Sdh inhibitors in various pathogens. Therefore, we consider these mutations to be target-site resistance mutations for these acaricidal SDH inhibitors.
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Affiliation(s)
- Naoya Sugimoto
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Biology Group, Health and Crop Sciences Research Laboratory, Sumitomo Chemical Co., Ltd, Takarazuka 665-8555, Japan.
| | - Akihiro Takahashi
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Rei Ihara
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Itoh
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000, Ghent, Belgium
| | - Masahiro Osakabe
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Chen Y, Bird L, Woolley L, Walsh T, Gordon K, Herron G. Linkage mapping an indoxacarb resistance locus in Helicoverpa armigera (Lepidoptera: Noctuidae) by genotype-by-sequencing. PEST MANAGEMENT SCIENCE 2020; 76:617-627. [PMID: 31313471 DOI: 10.1002/ps.5557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND A major challenge to sustainable agricultural pest control is the rapid evolution of insecticide resistance. This is caused by mechanisms that reduce insecticide efficacy. Understanding the genetic mechanisms of resistance is essential for DNA-based monitoring of resistance in field populations. One such insecticide is indoxacarb, an important selective control option for Helicoverpa armigera in a range of crops including grain, horticulture and cotton. Recently, a strain of H. armigera (GY7-39) resistant to indoxacarb (198-fold) was isolated from field-collected moth. RESULTS To identify the indoxacarb resistance locus, GY7-39 was backcrossed for six generations to susceptible strain New GR. In each generation, only resistant males were used to cross back to New GR. Genotype-by-sequencing was carried out on 95 H. armigera samples. In total, 13 203 tags with 8697 unique locations on the H. armigera genome were obtained. The indoxacarb resistance locus in strain GY7-39 was mapped to a 2.6 Mbp region on chromosome 16. In this region, two closely linked loci (IndoR1 and IndoR2) were found to be associated with indoxacarb resistant GY7-39. CONCLUSIONS We mapped indoxacarb resistance in GY7-39 to two closely linked loci IndoR1 and IndoR2 in a narrowed 2.6 Mbp region of H. armigera chromosome 16. The results provide essential background data for future genetic investigations including fine mapping of the indoxacarb resistance gene and the eventual development of an effective DNA-based diagnostic to support resistance management. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yizhou Chen
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Lisa Bird
- New South Wales Department of Primary Industries, Tamworth Agricultural Institute, Calala, Australia
| | - Lauren Woolley
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Tom Walsh
- CSIRO, Black Mountain Laboratories, Canberra, Australia
| | - Karl Gordon
- CSIRO, Black Mountain Laboratories, Canberra, Australia
| | - Grant Herron
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
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Johnston SE, Huisman J, Ellis PA, Pemberton JM. A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer ( Cervus elaphus). G3 (BETHESDA, MD.) 2017; 7:2859-2870. [PMID: 28667018 PMCID: PMC5555489 DOI: 10.1534/g3.117.044198] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/27/2017] [Indexed: 11/29/2022]
Abstract
High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion, and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7 cM and the genome-wide autosomal recombination rate was 1.04 cM/Mb. The female autosomal map length was 1.21 longer than that of males (2767.4 cM vs. 2280.8 cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement, and population management in red deer and related species.
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Affiliation(s)
- Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Jisca Huisman
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
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