Mosquitoes LTR retrotransposons: a deeper view into the genomic sequence of Culex quinquefasciatus

Abstract

A set of 67 novel LTR-retrotransposon has been identified by in silico analyses of the Culex quinquefasciatus genome using the LTR_STRUC program. The phylogenetic analysis shows that 29 novel and putatively functional LTR-retrotransposons detected belong to the Ty3/gypsy group. Our results demonstrate that, by considering only families containing potentially autonomous LTR-retrotransposons, they account for about 1% of the genome of C. quinquefasciatus. In previous studies it has been estimated that 29% of the genome of C. quinquefasciatus is occupied by mobile genetic elements.The potential role of retrotransposon insertions strictly associated with host genes is described and discussed along with the possible origin of a retrotransposon with peculiar Primer Binding Site region. Finally, we report the presence of a group of 38 retrotransposons, carrying tandem repeated sequences but lacking coding potential, and apparently lacking "master copy" elements from which they could have originated. The features of the repetitive sequences found in these non-autonomous LTR retrotransposons are described, and their possible role discussed.These results integrate the existing data on the genomics of an important virus-borne disease vector.

Figure 1. Evolutionary relationships of C. quinquefasciatus LTR-retrotransposons.

Phylogenetic relationships of the LTR retrotransposons based on the amino acids alignment of the conserved RT, RNase H and INT domains. The clades in which fall retrotransposons detected in this paper are indicated with different colors, along with the most common tRNA complementary to the PBS is indicated for each homogeneous group. Elements from this study are indicated as “cpgypsy_” followed by a number. AAGYPSY# elements are LTR retrotransposons identified in previous analyses . The N-J bootstrap values supporting the internal branches are indicated at the nodes. Only bootstrap values greater than 50% are reported. Bel-like elements were used as outgroup. Note that, for families composed of two or more copies (see table 1), representative elements (see file S1) were used for the phylogenetic analyses.

Figure 2. Evolutionary relationships of Osvaldo-like elements of C. quinquefasciatus LTR-retrotransposons.

Phylogenetic relationships of the Osvaldo-like retrotransposons based on the amino acids alignment of the conserved RT, RNase H and INT domains CPGYPSY5 and AAGYPSY# are LTR retrotransposons identified in previous analyses . Elements “gypsy ELE ###” were retrieved from the TEfam database. The N-J bootstrap values supporting the internal branches are indicated at the nodes. Only bootstrap values greater than 50% are reported. Bel-like elements were used as outgroup.

Figure 3. Organization of the LTR-PBS region of cqgypsy_1.

A) The tRNA sequences inserted into the 5′LTR of the cqgypsy_1 element. The LTR sequence is colored in red, while the PBS sequence is colored in blue. The red bar indicates the duplicated sequence surrounding the putative Twin element. Each of the tRNA halves of the putative Twin is highlighted in turquoise (tRNA^Lys) or in yellow (tRNA^Glu). The PBS is depicted in blue. B) tRNAscan output showing the secondary structure of the two halves of the insertion as a cloverleaf structure. C) Local alignment results of cqgypsy_1 with the gypsy_Ele180 and gypsy_Ele185. The aligned region correspond to the 5′LTR (red)/PBS(black) boundary.