Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans

We took advantage of the massive amount of sequence information generated by the Caenorhabditis elegans genome project to perform a comprehensive analysis of a group of over 100 related sequences that has allowed us to describe two new C. elegans non-LTR retrotransposons. We named them Sam and Frodo. We also determined that several highly divergent subfamilies of both elements exist in C. elegans. It is likely that several master copies have been active at the same time in C. elegans, although only a few copies of both Sam and Frodo have characteristics that are compatible with them being active today. We discuss whether it is more appropriate under these circumstances to define only 2 elements corresponding to the most divergent groups of sequences or up to 16, considering each subfamily a different element. The C. elegans elements are related to other previously described non-LTR retrotransposons (CRI, found in different vertebrates; SR1, from the trematode Schistosoma; Q and T1, from the mosquito Anopheles). All of these elements, according to the analysis of their reverse transcriptases, form a monophyletic cluster that we call the "T1/CR1 subgroup." Elements of this subgroup are thus ancient components of the genome of animal species. However, we discuss the possibility that these elements may occasionally be horizontally transmitted.