Open Access Highly Accessed Research article

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

Anna Cohuet1*, Sujatha Krishnakumar2, Frédéric Simard13, Isabelle Morlais13, Anastasios Koutsos45, Didier Fontenille1, Michael Mindrinos2 and Fotis C Kafatos4*

Author Affiliations

1 Institut de Recherche pour le Développement, UR 016, BP 64501, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France

2 Stanford Genome Technology Center, 855 California Avenue, Palo Alto CA 94304, USA

3 Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale, Laboratoire de Recherche sur le Paludisme, BP 288, Yaounde, Cameroon

4 Imperial College London, Division of Cell and Molecular Biology, Sir Alexander Fleming Building, South Kensington Campus, London, SW7 2AZ, UK

5 BMC-series Journals, BioMed Central, Middlesex House, 34-42 Cleveland Street, London W1T 4LB, UK

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BMC Genomics 2008, 9:227  doi:10.1186/1471-2164-9-227

Published: 19 May 2008



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.


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 (π) 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.


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.