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

Abstract

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.

Adaptation by copy number variation increases insecticide resistance in fall armyworms

“…This proportion is higher than that of SNVs (11.31%, 1,847,439/16,341,783, p < 2.2 × 10 -16 ; Fisher's exact test). The same trend was observed from mosquito, in which CNVs are overrepresented in gene-containing regions 8 .…”

“…Well-known detoxification genes include cytochrome P450s (CYPs) 3 , esterases 4 , Glutathione S-transferases (GSTs) 3 , UDP glucuronosyltransferases (UGTs) 5 , and oxidative stress genes 6 . 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 .…”

A high throughput multi-locus insecticide resistance marker panel for tracking resistance emergence and spread inAnopheles gambiae

“…We confirmed the role of a duplication by showing that the heterozygosity is associated with the presence of the Gste2 duplication Gstue_Dup7 (Lucas et al 2018). While the vast majority of Gstue_Dup7 alleles are heterologous, we also found evidence of a rare variant of Gstue_Dup7 in two samples where the duplication was homozygous for the 114T SNP.…”

“…gambiae and An. coluzzii from across SSA (Lucas et al 2018), but only one of these, Gstue_Dup1, was shown to be associated with the 114T mutation, being homologous for the mutant allele. The evolution of duplications in Gste2 may therefore mirror what has been found in Ace-1, where both homologous and heterologous duplications exist.…”

“…the duplication breakpoint. The position of the breakpoint was known from previous data (Lucas et al 2018) and primers were designed using NCBI Primer Blast (Ye et al 2012).…”