Mapping Transposable Elements in 16 Species of Anopheles (mosquitoes)
Mentor:Peter Arensburger, Assistant Professor, California State Polytechnic University, Pomona
The purpose of this study is to look for Transposable elements (TEs) in 16 different Anopheles species. All living organisms have TEs, but not all are expressed. TEs are special pieces of DNA that have the ability to move around within the genome of an organism on their own. TEs have a few key markers that we used to locate them. TEs use target sites to insert themselves into the DNA, once they have inserted themselves into the DNA they duplicate the target site and we get Target Site Duplications (TSD). TE’s also have Terminal Inverted Repeats (TIRs) where nucleotide sequences on both ends of the element are almost identical in sequence but are inverted. Discovering new TEs would be very useful in learning how they work in a living organism’s genome. Anopheles gambiae which has been sequenced and has known TEs present in its genome was used as our reference. Using Bioinformatics techniques we started with the genomes Anopheles albimanus, Anopheles dirus, and Anopheles funestus. To search through each genome, we used Perl scripts (computer algorithms) to look for key markers, the length of TIRs, the location of a TSD in association with the TIR, and the length of the open reading frame. The parameters for the Perl scripts were determined by which type of TE we were looking for. The types of TEs looked for were Tc/Mariner elements and hAT elements, a TE family, both of which have unique indicators in the TIRs and TSDs. The Perl scripts were run on each genome, and gave several sequences that could be potential TEs. We examined each sequence individually looking at its nucleotide content and its location within the genome. We found one possible hAT TE in Anopheles funestus and many possible Tc/Mariner TEs in Anopheles albimanus and Anopheles dirus.