Novel LINE elements from the coelacanth Latimeria menadoensis.

Retrotransposons are ubiquitous components of the DNA of many eukaryotic organisms. They move by an RNA intermediate and consist of two sub-types, the long terminal repeat (LTR) and the non-LTR retrotransposons. LTR retrotransposons have direct LTRs that range from ~100 bp to over 5 kb in size. Non-LTR retrotransposons consists of two sub-types, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). LINEs code for the enzyme reverse transcriptase, and many LINEs also code for an endonuclease. The analysis of LINEs as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data. The presence of a given retrotransposon in related taxa suggests their orthologues integration, while the absence of particular elements can be considered an ancestral trait. The "living fossil" Latimeria menadoensis, belonging to the order Coelacanthiformes, is a very interesting organism for the evolutionary history of vertebrates. Our study aims to seek LINEs elements in the genome of this organism, to obtain new information and molecular markers for a more precise definition of the phyletic relationships that exist between this species and those that gave rise to tetrapods. Initial results highlight the presence of LINE transposons in L. menadoensis. We have isolated by PCR amplification a genomic fragment (~600 bp long) that shows similarity to a reverse transcriptases RVT_1, and a second one (~1500 bp long) that contains a region with high homology to an Exo_endo_phos endonuclease (pfam 03372). Both these fragments seem to belong to the LINE elements family that has the typical architecture "Endonuclease/RNA Reverse transcriptase-dependent DNA polymerase".