Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers

We examined the diversity, evolution, and genomic organization of retroelem ents in a wide range of gymnosperms. In fetal, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newl y designed primers for gypsy-like retrotransposons and well-known primers f or copia-like retrotransposons; representatives of long interspersed nuclea r element (LINE) retroposons were also found. Gypsy and copia-like retroele ments are a major component of the gymnosperm genome, and in situ hybridiza tion showed that individual element families were widespread across the chr omosomes, consistent with dispersion and amplification via an RNA intermedi ate. Most of the retroelement families were widely distributed among the gy mnosperms, including species with wide taxonomic separation from the Northe rn and Southern Hemispheres. When the,gymnosperm sequences were analyzed to gether with retroelements from other species, the monophyletic origin of pl ant copia, gypsy, and LINE groups was well supported, with an additional cl ade including badnaviral and other, probably virus-related, plant sequences : as well as animal and fungal gypsy elements. Plant retroelements showed h igh diversity within the phylogenetic trees of both copia and gypsy RT doma ins, with, for example, retroelement sequences from Arabidopsis thaliana be ing present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conif ers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetu m), suggesting that much of the existing diversity was present early in pla nt evolution, or perhaps that horizontal transfer of sequences has occurred . Within the phylogenetic trees for both gypsy and copia, two clearly monop hyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The, results put the evolution of the large an d relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.