Selective Sweep Analysis in the Genomes of the 91-R and 91-C Drosophila melanogaster Strains Reveals Few of the â•ŸUsual Suspectsâ•Ž in Dichlorodiphenyltrichloroethane (DDT) Resistance

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 alteredMDR49 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. PLOS ONE | DOI:10.1371/journal.pone.0123066 March 31, 2015 1 / 15 OPEN ACCESS Citation: Steele LD, Coates B, Valero MC, Sun W, Seong KM, Muir WM, et al. (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. doi:10.1371/journal.pone.0123066 Academic Editor: Pedro Lagerblad Oliveira, Universidade Federal do Rio de Janeiro, BRAZIL Received: September 4, 2014 Accepted: February 17, 2015 Published: March 31, 2015 Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Data Availability Statement: The BAM files have been deposited at NCBI with accession number of SRP052046. Funding: The sequencing of the 91-R and 91-C genomes were paid for by the C.W. Kearns, C.L. Metcalf and W.P. Flint Endowment. A portion of research data analyses was supported by the United States Department of Agriculture, Agricultural Research Service (USDA-ARS; CRIS Project 362522000-017-00) and the Iowa Agriculture and Home Economics Experiment Station, Ames, IA (Project