Genetic diversity of the 16S rRNA and secY genes in phytoplasma strains detected in leek plants in Brazil

Leek is a vegetable crop cultivated in diverse geographic areas of the world. Leek plants exhibiting symptoms of stunting and twisted leaves, resulting in reduced size and loss of vigour, were observed in commercial fields located in the state of São Paulo, Brazil. Since these symptoms are suggestive of phytoplasma presence plants were analyzed to verify the presence of this pathogen in the affected plants. Amplification of genomic fragments of 1.6 kb from the 16S rRNA gene and 1.7 kb from the secY gene confirmed the presence of phytoplasmas in symptomatic plants. The results from virtual RFLP, similarity coefficient values, and phylogenetic analysis identified strains related to ‘Candidatus Phytoplasma pruni’ subgroup 16SrIII-J and ‘Ca. P. meliae’ subgroup 16SrXIII-E. In addition, three ‘Ca. P. meliae’ strains showed in the 16S rRNA gene variability and were differentiable from all the designed ribosomal subgroups. The analysis of secY gene presented greater genetic variation compared with 16S rRNA gene. However, this gene, although considered as a marker to differentiate biologically and/or ecologically closely related phytoplasmas, did not separate strains within the 16SrIII-J subgroup. These findings demonstrate that leek plants are new host species for phytoplasmas in the Brazilian agroecosystem.