Selective Sweep Analysis in the Genomes of the 91-R and 91-C Drosophila melanogaster Strains Reveals Few of the ‘Usual Suspects’ in Dichlorodiphenyltrichloroethane (DDT) Resistance

Abstract

Adaptation of insect phenotypes for survival after exposure to xenobiotics can result from selection at multiple loci with additive genetic effects. To the authors’ knowledge, no selective sweep analysis has been performed to identify such loci in highly dichlorodiphenyltrichloroethane (DDT) resistant insects. Here we compared a highly DDT resistant phenotype in the Drosophila melanogaster (Drosophila) 91-R strain to the DDT susceptible 91-C strain, both of common origin. Whole genome re-sequencing data from pools of individuals was generated separately for 91-R and 91-C, and mapped to the reference Drosophila genome assembly (v. 5.72). Thirteen major and three minor effect chromosome intervals with reduced nucleotide diversity (π) were identified only in the 91-R population. Estimates of Tajima's D (D) showed corresponding evidence of directional selection in these same genome regions of 91-R, however, no similar reductions in π or D estimates were detected in 91-C. An overabundance of non-synonymous proteins coding to synonymous changes were identified in putative open reading frames associated with 91-R. Except for NinaC and Cyp4g1, none of the identified genes were the ‘usual suspects’ previously observed to be associated with DDT resistance. Additionally, up-regulated ATP-binding cassette transporters have been previously associated with DDT resistance; however, here we identified a structurally altered MDR49 candidate resistance gene. The remaining fourteen genes have not previously been shown to be associated with DDT resistance. These results suggest hitherto unknown mechanisms of DDT resistance, most of which have been overlooked in previous transcriptional studies, with some genes having orthologs in mammals.

Comparative CYP‐omic analysis between the DDT‐susceptible and ‐resistant Drosophila melanogaster strains 91‐C and 91‐R

“…Three regions in the genome of 91-R were previously defined as having undergone a minor selective sweep that reduced nucleotide diversities under the influence of DDT selection …”

“…To the best of our knowledge, this study represents the first combined structural and functional analysis of variation in P450s between highly DDT‐resistant and ‐susceptible strains. Prior evidence suggests that high levels of DDT resistance in 91‐R are polygenic, with multiple SNPs in 13 genomic regions contributing to the DDT resistance phenotype . Although comparative, the detection of SNPs and overrepresentation of nonsynonymous changes suggest putative functional changes in response to selection.…”

“…This may have enabled them to lose some xenobiotic-metabolizing P450s to avoid the fitness cost of their expression in the absence of other such chemical or environmental stresses. The 91-R strain has been exposed to DDT selection, and thus it is understandable that specific P450s are probably needed more in 91-R than in 91-C. Additionally, in spite of evidence that selective sweeps have probably occurred in response to DDT selection in 91-R, 47 it is possible that genetic drift could have resulted in significant genetic variation in the relatively small number of individuals in the 91-C and 91-R laboratory populations. 85 While P450 enzymes play a critical role in the metabolism of endogenous and exogenous chemicals, including insecticides, 86 loss-of-function mutations do not result in catastrophic loss of fitness.…”

“…[44][45][46] These two strains were derived from a known common origin, but subsequent differences in the DDT selection schemes have provided a valuable resource for comparative analysis within the context of a model for studying xenobiotic resistance mechanisms on a genomic-wide scale. Indeed, these two strains formed the basis of a comparative genomic study that identified genome regions with significant variance in nucleotide fixation putatively attributable to the effects of differential selection, which included one region encoding Cyp4g1 47,48 and ATP-binding cassette transporters (ABC transporters) open reading frames. 47,49 Previously, Brandt et al showed that the P450 inhibitor piperonyl butoxide (PBO) drastically reduces (but does not eliminate) DDT resistance in D. melanogaster, providing further evidence that differential expression of P450 genes is a component of the DDT resistance phenotype.…”

“…Indeed, these two strains formed the basis of a comparative genomic study that identified genome regions with significant variance in nucleotide fixation putatively attributable to the effects of differential selection, which included one region encoding Cyp4g1 47,48 and ATP-binding cassette transporters (ABC transporters) open reading frames. 47,49 Previously, Brandt et al showed that the P450 inhibitor piperonyl butoxide (PBO) drastically reduces (but does not eliminate) DDT resistance in D. melanogaster, providing further evidence that differential expression of P450 genes is a component of the DDT resistance phenotype. 29 The current study expands on prior work performed in the DDT-resistant strain 91-R by investigating the structural and expression level (functional) variance across all P450 gene family members compared with that of its control strain, 91-C.…”