Effects of RNA editing on the coxI evolution and phylogeny reconstruction

CoxI genomic and cDNA sequences from gymnosperms and angiosperms were used to study the effects of RNA editing on gene evolution and phylogeny reconstruction. In six gymnosperms harboring edited coxI gene the number of nucleotide substitutions at 1^st, 2^nd and 3^rdcodon positions was similar. In contrast, in angiosperms, the number of nucleotide substitutions at 1^st and 2^nd codon positions was much lower than at the 3^rd. The coxI gene in long-lived gymnosperms evolved much faster than in annual angiosperms. This accelerated rate of nucleotide substitution in gymnosperms is due to accumulation of T-C substitutions at edited sites that can randomly appear at all three codon positions. Editing predominantly occurred at 1^st and 2^nd codon positions as a result 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 in concordance with their taxonomic positions. The trees based on polymorphic edited sites agreed with trees derived from complete sequence information. This indicates that edited sites are reliable sources of phylogenetic information especially for species that contain many edited sites. However, the fast evolution rate of coxI gene in gymnosperms has caused 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.