In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either
separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA
locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern
blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA
genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and
Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the
35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo
(∼30% of the species analysed), while the remaining exhibit separate
organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short
tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may
be encoded by the same (Ginkgo, Ephedra) or opposite
(Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition,
pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have
been largely homogenised across the genomes. Phylogenetic relationships based on the
comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at
least three times in the course of gymnosperm evolution. Frequent transpositions and
rearrangements of basic units indicate relatively relaxed selection pressures imposed on
genomic organisation of 5S genes in plants.