Prospects of DNA-based systems for differentiation and classification of phytoplasmas

During the last two decades, over 800 phytoplasma strains have been reported in association with several hundred plant diseases and numerous insect vectors. Research has yielded new knowledge about phytoplasma ecology and phylogenetic relationships. A taxonomic system has emerged, and perspectives on phytoplasma speciation have changed. Guidelines for naming new ‘Candidatus Phytoplasma’ species have been proposed; the16S rRNA gene was employed as the sole phylogenetic marker for species delineation. To date, 26 ‘Ca. Phytoplasma’ species have been named, forming the core framework of the emerging phytoplasma taxonomy. A classification system based on restriction fragment length polymorphism (RFLP) analysis of 16S rRNA gene sequences provides a simple, reliable, and rapid means to classify phytoplasmas on a large scale without a need to sequence the gene. The capacity of this classification system has been recently upgraded by the development of a computer-simulated RFLP analysis method. This approach has led to construction of the most comprehensive classification system for phytoplasmas to date. The concept of multi-gene sequence analysis for distinguishing phytoplasma species has emerged with the aim of overcoming deficiencies of the highly conserved 16S rRNA gene for delineating closely related phytoplasma species. Less conserved genes, such as ribosomal protein or secY, serve as phylogenetic markers for finer distinctions among phytoplasmas.