PHYLOGENETIC-RELATIONSHIPS OF REVERSE-TRANSCRIPTASE AND RNASE-H SEQUENCES AND ASPECTS OF GENOME STRUCTURE IN THE GYPSY GROUP OF RETROTRANSPOSONS

The gypsy group of long-terminal-repeat retrotransposons contains elem ents having the same order of enzyme domains in the pol gene as do ret roviruses. Elements in the gypsy group are now known from yeast, filam entous fungi, plants, insects, and echinoids. Reverse transcriptase an d RNase H amino acid sequences from elements in the gypsy group-includ ing the recently described SURL elements, TED, Cft1, and Ulysses,-were aligned and analyzed by using parsimony and bootstrapping methods, wi th plant caulimoviruses and/or retroviruses as outgroups. Clades suppo rted at the 95% level after bootstrapping include (1) 17.6 with 297 an d (2) all of the SURL elements together. Other likely relationships su pported at lower bootstrap confidence intervals include (1)SURL elemen ts with mag, (2) 17.6 and 297 with TED, and this collective group with 412 and gypsy, (3) Tf1 with Cft1, (4) IFG7 with Del, and (5) all of t he retrotransposons in the gypsy group together, to the exclusion of T y3. In contrast with an earlier analysis, our results place mag within the gypsy group rather than outside of a cluster that contains gypsy group retrotransposons and plant caulimoviruses. Several features of r etrotransposon genomes provide further support for some of the aforeme ntioned relationships. The union of SURL elements with mag is supporte d by the presence of two RNA binding sites in the nucleocapsid protein . Location of the tRNA primer binding site and the presence of a long open reading frame 3' to the pol gene support the 17.6-297-TED-412-gyp sy cluster.