A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster

In addition to previously characterized BS, Doc, F, G, I and Jockey elements, we have identified new non-LTR retrotransposons: Waldo, You and JuanDm. Waldo elements are related to mosquito RTI elements. You to the Drosophila I factor, and JuanDm to mosquito Juan-A and Juan-C. Interestingly, all JuanDm elements are highly homogeneous in sequence, suggesting that they are recent components of the Drosophila genome.The genome of D. melanogaster contains at least ten families of non-site-specific non-LTR retrotransposons representing three distinct clades. Many of these families contain potentially active members. Fine evolutionary analyses must await the more accurate sequences that are expected in the next future.Non-long terminal repeat (non-LTR) retrotransposons, also known as LINEs (long interspersed nuclear elements), make up a very large class of transposable elements that are present in most eukaryotes [1,2]. They transpose by reverse transcription of an RNA intermediate. They possess an open reading frame (ORF) with coding capacities for a protein with endonuclease, reverse transcriptase and sometimes RNase H activities. Many of them contain an additional ORF (ORF1) encoding a protein of an unknown function. Some non-LTR retrotransposons, such as R1 and R2 in arthropods, insert at specific sites in the genome [3,4], whereas the others do not show specific sites of insertion. The cleavage specificity of some elements such as R2 is the result of the activity of an endonuclease showing similarities to restriction enzymes [5,6]. The other elements, whether they are site-specific (like R1) or not (like mammalian L1 elements), have an endonuclease structurally related to apurinic/apyrimidinic (AP) endonucleases [7,8]. Non-LTR retrotransposons can be assigned to 12 clades on the basis of the sequences of their reverse transcriptase domains and appear to be as old as eukaryotes [2,9]. The chronology of the acquisition of the various enzymatic domains suggests that the