Non-LTR retrotransposons in mosquitoes: Diversity, evolution, and analysis of potentially active elements

This research focuses on non-Long Terminal Repeat (non-LTR) retrotransposons in the African malaria mosquito, Anopheles gambiae and other mosquito species. An unprecedented diversity of non-LTR retrotransposons (non-LTRs) was discovered by genome analysis in a recently released An. gambiae genome assembly. During this analysis, new computational tools were developed that can facilitate Transposable Element (TE) discovery in any genome. One hundred and four families were found by a reiterative and comprehensive search using the conserved reverse transcriptase (RT) domains of known non-LTRs from a number of organisms as the starting queries. These families, which are defined by at least 20% amino acid sequence divergence in their RT domains, range from a few to approximately 2000 copies and occupy at least 3% of the genome. An. gambiae non-LTRs represent 8 of the 15 previously defined clades, plus two novel clades, Loner and Outcast, raising the total number of known clades to 17. Five families were found belonging to the L1 clade, which had no invertebrate representatives until this study. All clades except one have families with sequence characteristics suggesting recent activity.; Juan, a non-LTR of the Jockey clade originally discovered in the mosquito Culex pipiens quinquefasciatus (Mouches et al. 1991), has been implicated in horizontal transfer in three non-sibling species of the Aedes genus (Mouches, Bensaadi, and Salvado 1992). PCR was used to obtain sequences from 18 mosquito species of six genera. Phylogenetic analysis demonstrates predominant vertical inheritance of Juan elements among these species. There is strong evidence from sequence analysis supporting the recent activity of Juan in several divergent species. We hypothesize that the sustained activity (versus quick inactivation) of non-LTRs in mosquitoes may contribute to the diversity we observe in the An. gambiae genome today.; TE display, a method similar to Amplified Fragment Length Polymorphism, was shown to be a highly specific and reproducible method to detect the insertion sites of TEs. TE display was also shown to be useful for the genome-wide identification of non-LTR insertions in individual mosquitoes and cell lines. A high degree of polymorphism was detected for two non-LTR families Ag_I-2 and Ag_Jen-1 in An. gambiae populations, which is consistent with expectations of active elements. (Abstract shortened by UMI.)...