Molecular evolution of phytoplasmas based on polymorphisms in the 16S rRNA genes and the 16/23S spacer regions

This paper describes the reclassification and molecular evolution of phytoplasmas based on nucleotide sequence analysis of the 16S rRNA and 16/23S spacer region. Analyses of the secondary structure of 16S rRNA among 23 phytoplasmas revealed 308 polymorphisms of which two thirds were located in nine highly variable regions. The 16/23S spacer region comprised two highly conserved regions and a highly conserved tRNA(Ile) gene. Nucleotide deletion/insertions of various lengths occurred only between the highly conserved regions, resulting in 16/23S spacer regions with varying lengths among different phytoplasmas. Phylogenetic analysis on the alignments of secondary structure of 16S rRNA established a tree with ten major groups that had high confidence values. The branching patterns and differences in the 16S rRNA sequence homology greater than 2.5% established 10 major groups among the 23 phytoplasmas. We hypothesize that phytoplasmas evolved independently from a common ancestor into two branches: one branch consisting of the aster yellows and stolbur groups, and the others as a second branch.