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Title: 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

Author
item STEELE, LAURA - University Of Illinois
item Coates, Brad
item QUIROS, CARMEN - University Of Illinois
item SUN, WEILIN - University Of Illinois
item SEONG, KEON MOOK - University Of Illinois
item MUIR, BILL - Purdue University
item CLARK, JOHN - University Of Massachusetts
item PITTENDRIGH, BARRY - University Of Illinois

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2015
Publication Date: 3/31/2015
Citation: Steele, L.D., Coates, B.S., Quiros, C.V., Sun, W., Seong, K., Muir, B., Clark, J.M., Pittendrigh, B.R. 2015. 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. PLoS One. 10(3):e0123066.

Interpretive Summary: The development and spread of insect populations that are resistant to chemical insecticides threaten the sustainability of agricultural production in the United States and worldwide. Both the insect species Drosophila melanogaster and the chemical insecticide dichlorodiphenyltrichloroethane (DDT) have become models for the study of evolving resistance traits in insect populations, and yield valuable insight into genetic and genome-wide mechanisms that translate into analogous resistance traits in crops pest species. The whole genome of a DDT resistant Drosphila melanogster strain was re-sequenced and variation across all chromosomes compared to that of DDT susceptible strains. From these analyses, 16 genome regions were linked to DDT resistance, and the wealth of gene functional information from this insect species were used to identify genes involved in the evolution of DDT resistance. Since DDT resistance often also confers cross-resistance to other classes of chemical insecticides, these data may likely be valuable for the study of genes linked similar traits in agricultural pest species. This information will be useful for government, university and private sector scientists that investigate insect resistance and who are concerned with durability of current insecticide chemistries used in agricultural production.

Technical Abstract: Adaptation of insect phenotypes for survival after exposure to xenobiotics can result from selection at multiple loci with additive genetic effects. A high level dichlorodiphenyltrichloroethane (DDT) resistance phenotype in the Drosophila melanogaster strain 91-R has resulted due to continuous laboratory selection over decades, whereas the 91-C strain had remained under non-selective conditions. Whole genome re-sequencing data from pools of individuals (Pool-seq) was generated separately for 91-R and 91-C, and mapped to the reference D. melanogaster genome assembly (v. 5.72). Thirteen major and three minor effect chromosome intervals with reduced nucleotide diversity (p) 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 p or D estimates were detected in 91-C. Ratios of synonymous to non-synonymous (protein coding) changes identified putative open reading frames (ORFs) in 91-R genome that were affected by directional/purifying selection. Annotations indicated that candidate genes predominantly function in gene regulation, signal transduction, ion transport, and neurotransmitter recycling. Interestingly, few of the genes identified in these selective sweeps where the ‘usual suspects’ previously observed to be associated with DDT resistance. These results suggest hitherto unknown mechanisms of DDT resistance.