Multilocus Gene Characterization of Phytoplasmas

Using 16S rRNA genes based primers for the identification of phytoplasmas associated with plants and insects has become the universally accepted method worldwide. The highly conserved ribosomal gene sequence (16Sr RNA) is being utilized as the key molecular tool for the identification and taxonomic classification of phytoplasma strains into “Candidatus Phytoplasma” species and ribosomal groups and subgroups. However, due to its highly conserved nature, the 16S rRNA gene is considered insufficient for finer differentiation of closely related but distinct phytoplasma strains. In recent years, several other multilocus moderately conserved genes have been employed for the classification and differentiation of phytoplasma strains. These additional loci are able to identify and differentiate between closely related strains of phytoplasmas that may appear similar based on the basis of 16S rRNA gene sequence analysis alone. In the present chapter, the utilization of several multilocus genes for the successful identification of phytoplasma strains within 16S ribosomal subgroups is discussed. These housekeeping genes have more phylogenetically informative characters than the 16S rRNA genes, thus increasing the resolving power for distinguishing genetically closely related phytoplasma strains.