| Summary: | <p>Abstract</p> <p>Background</p> <p>The genome of invertebrates is rich in retroelements which are structurally reminiscent of the retroviruses of vertebrates. Those containing three open reading frames (ORFs), including an <it>env</it>-like gene, may well be considered as endogenous retroviruses. Further support to this similarity has been provided by the ability of the <it>env</it>-like gene of <it>DmeGypV</it> (the <it>Gypsy</it> endogenous retrovirus of <it>Drosophila melanogaster</it>) to promote infection of Drosophila cells by a pseudotyped vertebrate retrovirus vector.</p> <p>Results</p> <p>To gain insights into their evolutionary story, a sample of thirteen insect endogenous retroviruses, which represents the largest sample analysed until now, was studied by computer-assisted comparison of the translated products of their <it>gag, pol</it> and <it>env</it> genes, as well as their LTR structural features. We found that the three phylogenetic trees based respectively on Gag, Pol and Env common motifs are congruent, which suggest a monophyletic origin for these elements.</p> <p>Conclusions</p> <p>We showed that most of the insect endogenous retroviruses belong to a major clade group which can be further divided into two main subgroups which also differ by the sequence of their primer binding sites (PBS). We propose to name <b>IERV-K</b> and <b>IERV-S</b> these two major subgroups of <b>I</b>nsect <b>E</b>ndogenous <b>R</b>etro <b>V</b>iruses (or <b>I</b>nsect <b>ER</b>ranti<b>V</b>irus, according to the ICTV nomenclature) which respectively use Lys and Ser tRNAs to prime reverse transcription.</p>
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