The evolution of Ty1-copia group retrotransposons in gymnosperms.

A diverse collection of Ty1-copia group retrotransposons has been characterized from the genome of Picea abies (Norway spruce) by degenerate PCR amplification of a region of the reverse transcriptase gene. The occurrence of these retrotransposable elements in the gymnosperms was investigated by Southern blot hybridization analysis. The distribution of the different retrotransposons across the gymnosperms varies greatly. All of the retrotransposon clones isolated are highly conserved within the Picea (spruce) genus, many are also present in Pinus (pine) and/or Abies (fir) genera, and some share strongly homologous sequences with one or more of cedar, larch, Sequoia, cypress, and Ginkgo. Further subclones of one of the most strongly conserved retrotransposon sequences, Tpa28, were obtained from Ginkgo and P. abies. Comparisons of individual sequence pairs between the two species show nucleotide cross-homologies of around 80%-85%, corresponding to nucleotide substitution rates similar to those of nuclear protein-coding genes. Analysis of Tpa28 consensus sequences reveals that strong purifying selection has acted on this retrotransposon in the lineages connecting Ginkgo and Picea. Collectively, these data suggest, first, that the evolution of the Ty1-copia retrotransposon group in the gymnosperms is dominated by germ line vertical transmission, with strong selection for reverse transcriptase sequence, and, second, that extinction of individual retrotransposon types has been comparatively rare in gymnosperm species lineages compared with angiosperms. If this very high level of sequence conservation is a general property of the retrotransposons, then their extreme sequence diversity implies that they are extremely ancient, and the major element lineages seen today may have arisen early in eukaryote evolution. The data are also consistent with horizontal transmission of particular retrotransposons between species, but such a mechanism is unnecessary to explain the results.