Effects of RNA editing on the coxI evolution and phylogeny reconstruction

Alfred E. Szmidt, Meng-Zhu Lu, and Xiao-Ru Wang

Euphytica (2001) 118: 9-18

For copy send email to: Alfred E. Szmidt

Abstract

CoxI genomic and cDNA sequences from gymnosperms and angiosperms were used to study the effects of RNA editing on gene evolution and phylogeny reconstruction. 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