SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system

Background: Anopheles innate immunity affects Plasmodium development and is a potential target of innovative malaria control strategies. The extent and distribution of nucleotide diversity in immunity genes might provide insights into the evolutionary forces that condition pathogen-vector interactions. The discovery of polymorphisms is an essential step towards association studies of susceptibility to infection. Results: We sequenced coding fragments of 72 immune related genes in natural populations of Anopheles gambiae and of 37 randomly chosen genes to provide a background measure of genetic diversity across the genome. Mean nucleotide diversity (pi) was 0.0092 in the A. gambiae S form, 0.0076 in the M form and 0.0064 in A. arabiensis. Within each species, no statistically significant differences in mean nucleotide diversity were detected between immune related and non immune related genes. Strong purifying selection was detected in genes of both categories, presumably reflecting strong functional constraints. Conclusion: Our results suggest similar patterns and rates of molecular evolution in immune and non-immune genes in A. gambiae. The 3,214 Single Nucleotide Polymorphisms (SNPs) that we identified are the first large set of Anopheles SNPs from fresh, field-collected material and are relevant markers for future phenotype-association studies.