The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications

Abstract

Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides’ target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies. We used an integrative approach, from genome to phenotype level, to investigate the influence of duplication architecture and gene-dosage on mosquito fitness. We found that both heterogeneous (i.e., one susceptible and one resistant ace-1 copy) and homogeneous (i.e., identical resistant copies) duplications segregated in field populations. The number of copies in homogeneous duplications was variable and positively correlated with acetylcholinesterase activity and resistance level. Determining the genomic structure of the duplicated region revealed that, in both types of duplication, ace-1 and 11 other genes formed tandem 203kb amplicons. We developed a diagnostic test for duplications, which showed that ace-1 was amplified in all 173 resistant mosquitoes analyzed (field-collected in several African countries), in heterogeneous or homogeneous duplications. Each type was associated with different fitness trade-offs: heterogeneous duplications conferred an intermediate phenotype (lower resistance and fitness costs), whereas homogeneous duplications tended to increase both resistance and fitness cost, in a complex manner. The type of duplication selected seemed thus to depend on the intensity and distribution of selection pressures. This versatility of trade-offs available through gene duplication highlights the importance of large mutation events in adaptation to environmental variation. This impressive adaptability could have a major impact on vector control in Africa.

Adaptive deletion in resistance gene duplications in the malaria vector Anopheles gambiae

“…Copy‐number variations (CNV) are indeed ubiquitous in natural populations (e.g., Freeman et al., 2006). While most of them are probably deleterious (Schrider et al., 2013), they can nonetheless play a crucial role in adaptation and evolution of genome complexity (Assogba et al., 2016; Katju & Bergthorsson, 2013; Kondrashov, 2012; Labbé, Berthomieu et al., 2007; Milesi, Weill, Lenormand, & Labbé, 2017; Schrider & Hahn, 2010). …”

“…On the contrary, heterogeneous duplications seem to be selected because the two alleles they carry can perform two different functions, by fixing the heterozygote advantage without segregation cost (Haldane, 1932; Milesi, Weill et al., 2017; Spofford, 1969). Such duplications have been documented in a few cases of insecticide resistance, the Rdl gene in Drosophila melanogaster (Remnant et al., 2013), or the ace‐1 gene in Anopheles gambiae and Culex pipiens (Assogba et al., 2016; Labbé, Berthomieu et al., 2007; Milesi, Assogba et al., 2017), where they associate one resistance and one susceptible copy of the gene. While still providing some resistance, this association partially alleviates the deleterious pleiotropic effects (or fitness cost) associated with the resistance allele (Assogba et al., 2015; Labbé et al., 2014; Milesi, Weill et al., 2017).…”

“…The chromosomal segment concerned by the duplication can indeed far exceed the gene of interest so that the resulting amplicons contain several other genes, as shown for example in Saccharomyces cerevisiae (Koszul, Caburet, Dujon, & Fischer, 2004), D. melanogaster (Remnant et al., 2013), and An. gambiae (Assogba et al., 2016). The present study is focused on this latter species, the major malaria vector in Africa, which provides a unique model system to investigate the dynamic and evolution of adaptive duplications: Both homogeneous and heterogeneous duplications of the ace‐1 gene can be found in this species, providing a large range of adaptive solutions for this mosquito to circumvent insecticide selective pressures (Figure 1a).…”

“…gambiae s.l . natural populations actually result from homogeneous duplications containing at least from 2 to 5 R copies (R x alleles, with x between 2 and 5, Figure 1a) (Assogba et al., 2016). The resulting trade‐offs depend on the number of R copies: higher R copy numbers confer higher levels of resistance, but the fitness cost also increases (Assogba et al., 2016).…”

“…In both homogeneous and heterogenous duplications, the amplicon borders are strictly identical, to the base: they consist of ~200 kb chromosome fragments containing ace‐1 , but also ten other genes. However, an internal deletion (ID) was identified in one of the amplicons of the three‐copies homogeneous duplication (R 3 *) found in the laboratory strain AcerkisR 3 (Figures 1 and 2); this ID was also found in genomic data from natural vector populations collected in Burkina Faso and Guinea (Assogba et al., 2016). Curiously, this deletion removes all the amplified genes, but ace‐1 , that is, in a R 3 * allele, there are three copies of ace‐1 , but only two copies of the ten other genes, as in D alleles (Figure 2).…”