GENOME-BASED STRATEGIES FOR DETECTION AND IDENTIFICATION OF PLANT PATHOGENIC PHYTOPLASMAS AND SPIROPLASMAS
Title: Phylogenetic analysis and delineation of phytoplasmas based on the secY gene
Submitted to: International Journal of Systematic and Evolutionary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 30, 2009
Publication Date: December 1, 2010
Citation: Lee, I., Bottner-Parker, K.D., Zhao, Y., Davis, R.E., Harrison, N. 2010. Phylogenetic analysis and delineation of phytoplasmas based on the secY gene. International Journal of Systematic and Evolutionary Microbiology. 60:2887-2897.
Interpretive Summary: Phytoplasma are very small bacteria that lack a cell wall and that cause several hundred economically important diseases in plants including potato, tomato, carrot, corn, grapevine, blackberry, strawberry, cherry, peach, apple, pear, grapevine, elm, palm, and ash. More than 1000 phytoplasma strains have been reported to be associated with various diseases worldwide. The different phytoplasmas infecting these plants, in many cases, are closely related to each other, and it has been difficult to distinguish them from one another by comparative analysis using a highly conserved gene. We studied a gene involved in protein transport for use in identifying the associated phytoplasmas. Analysis of this gene proved very useful for phytoplasma strain differentiation. As a result, this study revealed that phytoplasmas infecting apple, peach, and pear are distinct from one another. Each one represents a distinct species. Often, multiple phytoplasma strains were associated with a given disease. We proposed that multiple genes should be used for identification and classification of phytoplasma strains. The information will aid implementation of quarantine regulations, and it will help extension workers and plant diagnosticians to determine how to combat the diseases.
The secY gene, located in the operator-distal part of the spc ribosomal protein operon, codes for a protein translocase subunit secY. The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy for delineating phytoplasma strains in each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on secY gene permitted finer differentiation of phytoplasma strains, however. The secY gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. The high resolving power makes the secY gene a better genetic marker for differentiating closely related phytoplasma strains based on RFLP analysis. This study also revealed two heterogeneous spc operons present in the phytoplasma clade. This finding may have a significant implication in phytoplasma evolution.