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.