O'Loughlin, S. M. | Search bioRxiv

bioRxiv2023

Whole-genome sequencing of major malaria vectors reveals the evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso

Intensive deployment of insecticide based malaria vector control tools results in the rapid evolution of phenotypes resistant to these chemicals. Understanding this process on the genomic level is essential for the deployment of successful interventions. Using whole genome sequencing data of 1409 individual An. Gambiae s.l. collected from 2012 to 2017, we investigated the change in genetic structure and the evolution of the insecticide resistance variants in natural populations over time and space. The results showed similar and constant nucleotide diversity and negative Tajimas D between An. gambiae s.s. and An. coluzzii. PCA and FST showed a clear genetic structure in the An. gambiae s.l. species. Genome-wide FST and H12 scans identified genomic regions under divergent selection and also having an implication in the adaptations to ecological changes. Novel voltage-gated sodium channel pyrethroid resistance target-site alleles (V402L, I1527T) were identified at increasing frequencies alongside the established kdr alleles (Vgsc-L995F, Vgsc-L995S and N1570Y) within the An. gambiae s.l. populations. Organophosphate metabolic resistance markers were also identified, at increasing frequencies, within the An. gambiae s.s. populations from 2012 to 2017, including the SNP Ace1-G280S and its associated duplication. Variants simultaneously identified in the same vector populations raise concerns about the long-term efficacy of new-generation bednets and the recently introduced organophosphate pirimiphos-methyl indoor residual spraying. These findings highlighted the benefit of genomic malaria vector surveillance for the detection of new insecticide resistance variants, the monitoring of the existing resistance variants, and also to get insights into the evolutionary processes driving insecticide resistance. Author SummaryGenomic surveillance of malaria vectors is crucial for understanding the genetic variation in natural vector populations and also guiding the implementation of novel and innovative vector control tools. Application of sequencing technologies in vector studies provide insights on the genetic and evolutionary phenomena of vectors that could have impact on vector control strategies. By analyzing the whole genome data of 1409 wild An. gambiae s.l. mosquito collected between 2012 and 2017, we showed an emergence of novel insecticide resistance markers alongside increasing frequencies of existing insecticide resistance variants over time in Burkina Faso. We showed the benefit of genomic surveillance of malaria vectors for the monitoring of the insecticide resistance variants and also providing insights into the evolutionary processes driving insecticide resistance.

evolutionary biology↗

bioRxiv2021

Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control.

DNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements has emerged in the development of gene drives to control mosquito populations. Many gene drives work by recognising and inserting at a specific target sequence in the genome, often imposing a reproductive load as a consequence. They can therefore select for target sequence variants that provide resistance to the drive. Focusing on highly conserved, highly constrained sequences lowers the probability that variant, gene drive-resistant alleles can be tolerated. Here we search for conserved sequences of 18bp and over in an alignment of 21 Anopheles genomes, spanning an evolutionary timescale of 100 million years, and characterise the resulting sequences according to their location and function. Over 8000 ultra-conserved elements were found across the alignment, with a maximum length of 164 bp. Length-corrected gene ontology analysis revealed that genes containing Anopheles ultra-conserved elements were over-represented in categories with structural or nucleotide binding functions. Known insect transcription factor binding sites were found in 48% of intergenic Anopheles ultra-conserved elements. When we looked at the genome sequences of 1142 wild-caught mosquitoes we found that 15% of the Anopheles ultra-conserved elements contained no polymorphisms. Our list of Anopheles ultra-conserved elements should provide a valuable starting point for the selection and testing of new targets for gene-drive modification in the mosquitoes that transmit malaria.

genomics↗