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.
Highlights
Transposable elements are ubiquitous component of eukaryotic genomes and, besides their mutagenic role [1], they are considered as the major source of variability that can change genomes and their expression, either considering short term or large evolutionary scale time
The genome sequence of C. quinquefasciatus was downloaded from the Broad Institute website and scanned with the LTR_STRUC program [21] using the default parameters. 1179 putative retrotransposon sequences obtained as output were subjected to an ‘‘all against all’’ BLAST in order to group sequences with % identity greater than 98% over a sequence of at least 1 Kb. 157 groups containing at least one sequences were obtained after this step
In this paper we present data from the LTR_STRUC scan of the Culex quinquefasciatus genome
Summary
Transposable elements are ubiquitous component of eukaryotic genomes and, besides their mutagenic role [1], they are considered as the major source of variability that can change genomes and their expression, either considering short term or large evolutionary scale time. The great amount of sequence data produced have led to the identification of novel families of mobile genetic elements and posed a problem concerning their classification [2,3]. Looking at their transposition mechanism, transposons can be classified into two main classes [4]. Retrotransposons are major components of eukaryotic genomes; they are among the strongest evolutionary driving force acting on the genomes [5], and are potentially able to change gene expression patterns [6] [7]. Their ability to inflate eukaryotic genome size [8] is at the basis for their use as molecular markers in organisms of socio-economic interest [9]
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