Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes.

A number of recent papers report that standing genetic variation in natural populations includes ubiquitous polymorphisms within target sites for Cas9-based gene drive (CGD) and that these "drive resistant alleles" (DRA) preclude the successful application of CGD for managing these populations. Here we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that ~90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of ≥1.0%. We conclude that the abundance of conserved target sites in mosquito genomes and the inherent flexibility in CGD design obviates the concern that DRAs present in the standing genetic variation of mosquito populations will be detrimental to the deployment of this technology for population modification strategies

The origin of island populations of the African malaria mosquito, Anopheles coluzzii

Funding Information: This work was supported by grants from the UC Irvine Malaria Initiative Program, Open Philanthropy and NIH R56 grant (R56AI130277). We thank the National Malaria Control Program personnel from São Tomé and Príncipe and, Ministry of Health in São Tomé and Príncipe who facilitated our field collections in São Tomé. We thank the Centre International de Recherches Médicales de Franceville (Franceville, Gabon) for the collections in Gabon. Publisher Copyright: © 2021, The Author(s).Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species’ geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (FST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies.publishersversionpublishe

Complete mitogenome sequence of Aedes (Stegomyia) aegypti derived from field isolates from California and South Africa

The Aedes aegypti mitogenome (Mt) sequences of field isolates from California and South Africa revealed a deletion between position 14,522 and 14,659 of the Mt contig of the AaegL5 reference genome. The length of the mitogenome of the California isolate was 16,659 bp and had 99.0% similarity with the AaegL5 Mt contig. The South African isolate sequence was 16,600 bp long and had 97.9% similarity with the reference. The region between 1496 and 1664 bp is similar to a nuclear pseudogene that might be a copy of a portion of the mitochondrial genome.Defense Advanced Research Projects Agency (DARPA) Safe Gene Program (HR0011-17-2-0047), Centers for Disease Control and Prevention (CDC) grant for the Pacific Southwest Regional Center of Excellence for Vector-Borne Diseases (Cooperative Agreement U01CK000516), and University of California Davis School of Veterinary Medicine Vector-Borne Disease Pilot Grant Program (2016–2017).https://www.tandfonline.com/loi/tmdn20am2019Medical Virolog

Complete mitogenome sequence of Aedes (Stegomyia) aegypti derived from field isolates from California and South Africa

The Aedes aegypti mitogenome (Mt) sequences of field isolates from California and South Africa revealed a deletion between position 14,522 and 14,659 of the Mt contig of the AaegL5 reference genome. The length of the mitogenome of the California isolate was 16,659 bp and had 99.0% similarity with the AaegL5 Mt contig. The South African isolate sequence was 16,600 bp long and had 97.9% similarity with the reference. The region between 1496 and 1664 bp is similar to a nuclear pseudogene that might be a copy of a portion of the mitochondrial genome.Defense Advanced Research Projects Agency (DARPA) Safe Gene Program (HR0011-17-2-0047), Centers for Disease Control and Prevention (CDC) grant for the Pacific Southwest Regional Center of Excellence for Vector-Borne Diseases (Cooperative Agreement U01CK000516), and University of California Davis School of Veterinary Medicine Vector-Borne Disease Pilot Grant Program (2016–2017).https://www.tandfonline.com/loi/tmdn20am2019Medical Virolog

Introgression between Anopheles gambiae and Anopheles coluzzii in Burkina Faso and its associations with kdr resistance and Plasmodium infection

Background: Insecticide resistance in Anopheles coluzzii mosquitoes has become widespread throughout West Africa including in Burkina Faso. The insecticide resistance allele (kdr or L1014F) is a prime indicator that is highly correlated with phenotypic resistance in West Africa. Studies from Benin, Ghana and Mali have suggested that the source of the L1014F is introgression of the 2L divergence island via interspecific hybridization with Anopheles gambiae. The goal of this study was to characterize local mosquito populations in the Nouna Department, Burkina Faso with respect to: (i) the extent of introgression between An. coluzzii and An. gambiae, (ii) the frequency of the L1014F mutation and (iii) Plasmodium infection rates. Methods: A total of 95 mosquitoes were collected from ten sites surrounding Nouna town in Kossi Province, Burkina Faso in 2012. The species composition, the extent of introgression in An. coluzzii mosquitoes and their Plasmodium infection rates were identified with a modified version of the “Divergence Island SNP” (DIS) genotyping assay. Results: The mosquito collection contained 70.5% An. coluzzii, 89.3% of which carried a 3 Mb genomic region on the 2L chromosome with L1014F insecticide resistance mutation that was introgressed from An. gambiae. In addition, 22.4% in the introgressed An. coluzzii specimens were infected with Plasmodium falciparum, whereas none of the non-introgressed (“pure”) An. coluzzii were infected. Conclusion: This paper is the first report providing divergence island SNP genotypes for natural population of Burkina Faso and corresponding Plasmodium infection rates. These observations warrant further study and could have a major impact on future malaria control strategies in Burkina Faso

Model-based quantification of metabolic interactions from dynamic microbial-community data

An important challenge in microbial ecology is to infer metabolic-exchange fluxes between growing microbial species from community-level data, concerning species abundances and metabolite concentrations. Here we apply a model-based approach to integrate such experimental data and thereby infer metabolic-exchange fluxes. We designed a synthetic anaerobic co-culture of Clostridium acetobutylicum and Wolinella succinogenes that interact via interspecies hydrogen transfer and applied different environmental conditions for which we expected the metabolic-exchange rates to change. We used stoichiometric models of the metabolism of the two microorganisms that represents our current physiological understanding and found that this understanding - the model - is sufficient to infer the identity and magnitude of the metabolic-exchange fluxes and it suggested unexpected interactions. Where the model could not fit all experimental data, it indicates specific requirement for further physiological studies. We show that the nitrogen source influences the rate of interspecies hydrogen transfer in the co-culture. Additionally, the model can predict the intracellular fluxes and optimal metabolic exchange rates, which can point to engineering strategies. This study therefore offers a realistic illustration of the strengths and weaknesses of modelbased integration of heterogenous data that makes inference of metabolic-exchange fluxes possible from community-level experimental data

Complete mitogenome sequence of Aedes (Stegomyia) aegypti derived from field isolates from California and South Africa.

The Aedes aegypti mitogenome (Mt) sequences of field isolates from California and South Africa revealed a deletion between position 14,522 and 14,659 of the Mt contig of the AaegL5 reference genome. The length of the mitogenome of the California isolate was 16,659 bp and had 99.0% similarity with the AaegL5 Mt contig. The South African isolate sequence was 16,600 bp long and had 97.9% similarity with the reference. The region between 1496 and 1664 bp is similar to a nuclear pseudogene that might be a copy of a portion of the mitochondrial genome