Systematic screening of Anopheles mosquito genomes yields evidence for a major clade of Pao-like retrotransposons

We developed a degenerate PCR procedure to simultaneously amplify products from divergent retrotransposon families within the genomes of Anopheles mosquitoes. The procedure required cloning of multiple PCR products, but more than half of the clones subsequently sequenced were of retrotransposon origin. These included Copia-like and LINE retrotransposons, as well as the first Gypsy-like retrotransposons reported from mosquitoes. Furthermore, some Anopheles retrotransposon sequences showed similarity to the divergent Pao element from the silkmoth Bombyx mori. Phylogenetic analyses provided consistently strong bootstrap support (> 95%) for a major clade of Pao-like retrotransposons, which includes five mosquito sequences and the recently discovered Drosophila retrotransposons BEL and ninja. This appears to represent a new family of Pao-like LTR-retrotransposons distinct from the Copia and Gypsy families.