Structural variation at the TEP anti-pathogen locus in African malaria mosquitoes

Several species of mosquito in the Anopheles gambiae species complex are highly efficient vectors of malaria in sub-Saharan Africa. Two of these species, An. coluzii and An. gambiae, have only recently been elevated to the level of separate species, and were previously thought to be separate forms of the same species. Genome scans have revealed a region of high divergence on the left arm of the third chromosome (3L), containing at least 6 genes of the thioester-containing protein (TEP) family, which have been implicated in the innate immune response.  Interestingly, An. coluzzii populations from Mali and Burkina Faso are fixed for an allele at TEP1 – r^B, not present in sympatric An. gambiae populations – that confers additional resistance to the malaria parasite.  To annotate the TEP Anti-Pathogen Locus (TAPL) and identify structural variation among the three known haplotypes – r^B, r^A, and S – in the TAPL region, I have sequenced BAC clones of each of the three haplotypes and aligned them to each other.  These alignments indicate several significant structural differences between the three haplotypes, including a duplication in one haplotype that has resulted in the creation of a chimeric TEP gene.