Identification and phylogenetic analysis of gypsy-type retrotransposons inthe plant kingdom

PCR was performed with degenerate primers which hybridized to the homologou s sequences in the reverse transcriptase (rt) genes of gypsy-type retrotran sposons from rice (RIRE3, RIRE8 and RIRE2), using total DNA samples from va rious plants (monocots, dicots, pine, ginkgo, horsetail, liverwort and alga e) as templates. Cloning and sequencing showed that the amplified fragments had various degrees of homology to the rt sequences of rice retrotransposo ns. Phylogenetic analysis showed that these retrotransposon homologues and some additional gypsy-type retrotransposons previously identified from plan ts could be classified into two families, A and B. In each family, the retr otransposons were further classifiable into several subfamilies. Interestin gly, retrotransposons from a single or related plant species were clustered in each subfamily. This indicates that sequence divergence during vertical transmission has been a major influence on the evolution of gypsy-type ret rotransposons in plants. The retrotransposons isolated from one plant speci es could often be classified into the two families. This indicates that the gypsy-type retrotransposons of a family evolved independently within a spe cies without affecting the evolution of retrotransposons of the other famil y. Retrotransposons in each subfamily are characterized by the lengths of L TR, by the nucleotide sequences in the terminal regions of LTRs, and by the PBS (primer binding site) sequence complementary to the 3' sequence of a p articular tRNA species.