title: RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs.
abstract: BACKGROUND
  The extensive use of pyrethroids for control of malaria vectors, driven by their cost, efficacy and safety, has led to widespread resistance. To favor their sustainable use, the World Health Organization (WHO) formulated an insecticide resistance management plan, which includes the identification of the mechanisms of resistance and resistance surveillance. Recognized physiological mechanisms of resistance include target site mutations in the para voltage-gated sodium channel, metabolic detoxification and penetration resistance. Such understanding of resistance mechanisms has allowed the development of resistance monitoring tools, including genotyping of the kdr mutation L1014F/S in the para gene.
  
  
  METHODS
  The sequence-based technique RNA-seq was applied to study changes in the transcriptome of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from the Western Province of Kenya. The resulting gene expression profiles were compared to data in the most recent literature to derive a list of candidate resistance genes. RNA-seq data were analyzed also to identify sequence polymorphisms linked to resistance.
  
  
  RESULTS
  A total of five candidate-resistance genes (AGAP04177, AGAP004572, AGAP008840, AGAP007530 and AGAP013036) were identified with altered expression between resistant and susceptible mosquitoes from West and East Africa. A change from G to C at position 36043997 of chromosome 3R resulting in A101G of the sulfotransferase gene AGAP009551 was significantly associated with the resistance phenotype (odds ratio: 5.10). The kdr L1014S mutation was detected at similar frequencies in both phenotypically resistant and susceptible mosquitoes, suggesting it is no longer fully predictive of the resistant phenotype.
  
  
  CONCLUSIONS
  Overall, these results support the conclusion that resistance to pyrethroids is a complex and evolving phenotype, dependent on multiple gene functions including, but not limited to, metabolic detoxification. Functional convergence among metabolic detoxification genes may exist, with the role of each gene being modulated by the life history and selection pressure on mosquito populations. As a consequence, biochemical assays that quantify overall enzyme activity may be a more suitable method for predicting metabolic resistance than gene-based assays.
authors.affiliation: Program in Public Health, University of California, Irvine, CA, USA. m.bonizzoni@unipv.it.|Department of Biology and Biotechnology, University of Pavia, Pavia, Italy. m.bonizzoni@unipv.it.
authors.forename: Mariangela
authors.initials: M
authors.lastname: Bonizzoni
authors.affiliation: Centre for Global health Research, Kenya Medical Research Institute, Kisumu, Kenya. ericochomo@yahoo.com.
authors.forename: Eric
authors.initials: E
authors.lastname: Ochomo
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA. gus.dunn@yale.edu.
authors.forename: William Augustine
authors.initials: WA
authors.lastname: Dunn
authors.affiliation: Bioinformatics Core of the UC Davis Genome Center, University of California, Davis, CA, 95616, USA. mtbritton@ucdavis.edu.
authors.forename: Monica
authors.initials: M
authors.lastname: Britton
authors.affiliation: School of Health Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya. yaw_afrane@yahoo.com.
authors.forename: Yaw
authors.initials: Y
authors.lastname: Afrane
authors.affiliation: Program in Public Health, University of California, Irvine, CA, USA. zhoug@uci.edu.
authors.forename: Guofa
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Delta-9 Technologies, San Diego, CA, 92101, USA. jhartsel@gmail.com.
authors.forename: Joshua
authors.initials: J
authors.lastname: Hartsel
authors.affiliation: Program in Public Health, University of California, Irvine, CA, USA. mingchil@uci.edu.
authors.forename: Ming-Chieh
authors.initials: MC
authors.lastname: Lee
authors.affiliation: Program in Public Health, University of California, Irvine, CA, USA. jiabax1@uci.edu.
authors.forename: Jiabao
authors.initials: J
authors.lastname: Xu
authors.affiliation: Centre for Global health Research, Kenya Medical Research Institute, Kisumu, Kenya. Githeko@yahoo.com.
authors.forename: Andrew
authors.initials: A
authors.lastname: Githeko
authors.affiliation: Bioinformatics Core of the UC Davis Genome Center, University of California, Davis, CA, 95616, USA. joseph.fass@gmail.com.
authors.forename: Joseph
authors.initials: J
authors.lastname: Fass
authors.affiliation: Program in Public Health, University of California, Irvine, CA, USA. guiyuny@uci.edu.
authors.forename: Guiyun
authors.initials: G
authors.lastname: Yan
mesh_terms: D000818:Animals; D000852:Anopheles / Q000187:drug effects* / Q000235:genetics*; D020869:Gene Expression Profiling; D017344:Genes, Insect; D007305:Insecticide Resistance; D007306:Insecticides / Q000494:pharmacology*; D007630:Kenya; D020641:Polymorphism, Single Nucleotide; D011722:Pyrethrins / Q000494:pharmacology*; D017423:Sequence Analysis, RNA
chemical_list: D007306:Insecticides; D011722:Pyrethrins