Copy number variation (CNV) and insecticide resistance in mosquitoes: evolving knowledge or an evolving problem?

Weetman, David; Djogbenou, Luc; Lucas, Eric R.

doi:10.1016/j.cois.2018.04.005

Cited by 65 publications

(58 citation statements)

References 52 publications

(74 reference statements)

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“…Previous studies in marine fishes supported a role for CNVs in freeze resistance (Hew et al, 1988;Hayes et al, 1991, Chen et al, 2008Desjardins et al, 2012). For instance, Hayes et al (1991) (Faucon et al, 2017, Weetman et al, 2018. Furthermore, multiple gene copy number have been highlighted as substantial drivers of gene expression differences between populations of three-spined stickleback (Gasterosteus aculeatus), which facilitate phenotypic variation and habitat-specific selection to contrasted environments (Huang et al, 2019).…”

Section: Cnv-environment Associations Are Stronger Than Snp-environmementioning

confidence: 97%

“…Several studies have shown distinct roles of CNVs in local adaptation in terrestrial plants and animals (e.g. Tigano et al, 2018;Weetman et al, 2018;Bazzicalupo et al, 2019;Nelson et al, 2018;Prunier et al, 2019;Ruytinx et al, 2019) but empirical studies on CNVs in marine systems remain limited. Previous studies in marine fishes supported a role for CNVs in freeze resistance (Hew et al, 1988;Hayes et al, 1991, Chen et al, 2008Desjardins et al, 2012).…”

Section: Cnv-environment Associations Are Stronger Than Snp-environmementioning

confidence: 99%

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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Dorant

Cayuela

Wellband

et al. 2020

Preprint

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Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. Yet, our knowledge on genotypic variation and evolution is often limited to single nucleotide polymorphism (SNPs) and the role of CNVs has been overlooked in non-model species, partly due to their challenging identification until recently. Here, we document the usefulness of reducedrepresentation sequencing data (RAD-seq) to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs accounts for higher genetic differentiation than SNP markers. Contrary to SNPs for which no association was found, genetic-environment association revealed that 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal than SNPs.Our study provides the means to study CNVs in non-model species and underlines the importance to consider structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.

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Section: Cnv-environment Associations Are Stronger Than Snp-environmementioning

confidence: 97%

Section: Cnv-environment Associations Are Stronger Than Snp-environmementioning

confidence: 99%

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Dorant

Cayuela

Wellband

et al. 2020

Preprint

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“…The copy number variation (CNV) of these detoxication genes and associated positive selection have been reported from several insect pest species, including mosquitoes (Anopheles gambiae) 7,8 , Tobacco cutworm (Spodoptera litura) 9 , and fall armyworms (S. frugiperda) 10 . These genetic mechanisms are assumed to be associated with insecticide resistance 11 .…”

Section: Inroductionmentioning

confidence: 99%

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Nam

Gimenez

Hilliou³

et al. 2019

Preprint

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Insecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.

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“…CNVs thus have an opportunity to contribute to the selective response to these pressures, providing a context in which their importance can be assessed. Second, CNVs can play a key role in the evolution of insecticide resistance due to their ability to affect gene expression and allow co-expression of wild-type and mutant alleles [10,11]. Despite nearly two decades of genetic research into insecticide resistance, known resistance-associated SNPs are still unable to explain much of the variance in insecticide resistance [12].…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes

Lucas

Miles

Harding³

et al. 2018

Preprint

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BackgroundPolymorphisms in the copy number of a genetic region can influence gene expression, coding sequence and zygosity, making them powerful actors in the evolutionary process. Copy number variants (CNVs) are however understudied, being more difficult to detect than single nucleotide polymorphisms. We take advantage of the intense selective pressures on the major malaria vector Anopheles gambiae, caused by the widespread use of insecticides for malaria control, to investigate the role of CNVs in the evolution of insecticide resistance.ResultsUsing the whole-genome sequencing data from 1142 samples in the An. gambiae 1000 genomes project, we identified 1557 independent increases in copy number, encompassing a total of 267 genes, which were enriched for gene families linked to metabolic insecticide resistance. The five major candidate genes for metabolic resistance were all found in at least one CNV, and were often the target of multiple independent CNVs, reaching as many as 16 CNVs in Cyp9k1. These CNVs have furthermore been spreading due to positive selection, indicated by high local CNV frequencies and extended haplotype homozygosity.ConclusionsOur results demonstrate the importance of CNVs in the response to selection, with CNVs being closely associated with genes involved in the evolution of resistance to insecticides, highlighting the urgent need to identify their relative contributions to resistance and to track their spread as the application of insecticide in malaria endemic countries intensifies. Our detailed descriptions of CNVs found across the species range provides the tools to do so.

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Copy number variation (CNV) and insecticide resistance in mosquitoes: evolving knowledge or an evolving problem?

Cited by 65 publications

References 52 publications

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Whole genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes

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