For copy send email to: Alfred E. Szmidt
CoxI genomic and cDNA sequences from gymnosperms and angiosperms
were used to study the effects of RNA editing on gene evolution and
There were distinct differences between gymnosperms and angiosperms with
respect to the number of nucleotide substitutions at individual codon
positions and the effect of editing. In six gymnosperms harbouring
edited coxI gene the number of nucleotide substitutions at first,
second and third positions of the codons was similar. In contrast,
in angiosperms, the number of nucleotide substitutions at first and
second positions of the codons was much lower than at the third.
Contrary to previous suggestions, we found that the coxI
gene in long-lived gymnosperms is evolving much faster than in
angiosperms which have much shorter generation time. In our opinion,
the observed accelerated rate of nucleotide substitution on the coxI
gene in gymnosperms is due to random, free accumulation of T-C substitutions
at edited sites. It thus appears that accelerated sequence evolution caused
by an intensive editing can override slowdown caused by long generation time.
These results provide further evidence for a considerable heterogeneity
of sequence dynamics among different mitochondrial genes and plant lineages.
The occurrence of such redundant synonymous editing indicates that
edited Cs can randomly appear at all three codon positions, and that
their predominance at first and second codon positions is due to
'purifying' effect of selection against nonsynonymous T-C substitutions
and other types of mutations.
The tree topologies for the investigated species based on genomic
DNA data were generally in concordance with their taxonomic positions.
The trees based on polymorphic edited sites were concordant with trees
derived from complete sequence information. This result indicates that
contrary to some earlier suggestions, edited sites are reliable sources
of phylogenetic information especially for species that contain many
edited sites. However, the fast evolution rate of the coxI gene
in gymnosperms has lead to the long branches in the phylogenetic trees.
The inclusion of the species with a processed paralog i.e., edited form
of the coxI gene, affected the topology of phylogenetic trees,
especially when the taxon with a processed paralog was closely related
to the other species analyzed. The number of informative nucleotides
in cDNA was much lower than in genomic DNA sequences. Consequently,
phylogenetic trees based on cDNA sequences were poorly resolved.
Keywords:gymnosperms, mitochondrial DNA, phylogeny, processed paralog, RNA editing.
by Alfred E. Szmidt