Evaluating the effect of tuf and secA gene sequence length for discrimination of phytoplasmas

Phytoplasmas are a major liming factor to the growth and production of many plant species worldwide. Most studies have used the conserved 16S rRNA gene for phytoplasma identification and classification. The efficiency of the tuf and secA genes length in the characterization of phytoplasmas was evaluated by designing universal primers to amplify the long and short tuf (740 bp and 414 bp) and secA (1232 bp and 536 bp) genes from the phytoplasma 16SrII-A and -D sub-groups, which are closely related phytoplasma strains. The neighbour joining (NJ) and the maximum likelihood (ML) methods were used to test the accuracy and stability of the phylogenetic trees. The NJ and ML phylogenetic trees from the long and short DNA sequences of the 16S rDNA, tuf, and secA genes produced two major clades (WB and AS). The NJ and ML phylogenetic trees showed high similarity in their differentiation between and within the 16S phytoplasma groups. This study indicates that the long DNA sequences of tuf and secA genes produced phylogenetic trees with higher resolution and separated very closely related phytoplasma groups. The accurate characterization of phytoplasmas is important for epidemiological studies and in disease management.