Multilocus sequence typing and phylogenetic analysis revealed two distinct almond witches’‐broom phytoplasma subpopulations in Iran

During a field survey conducted in different geographical regions of Iran, phytoplasma‐like symptoms were observed in peach, almond, wild almond and GF‐677 rootstock. Based on 16S rDNA amplification, followed by nucleotide sequence and phylogenetic analyses, almond witches’‐broom (AlmWB) phytoplasma strains were found in association with symptomatic plants. Based on the single nucleotide polymorphisms within 16S rDNA sequence, most of the Iranian AlmWB phytoplasma strains were distinguished from the Lebanese strains. Further molecular typing, based on sequence and phylogenetic analyses of rplV‐rpsC (ribosomal proteins) and imp (immunodominant membrane protein) genes, indicated that AlmWB phytoplasma strains can be differentiated in two subpopulations: Ir, including exclusively Iranian strains, and Lb, comprising strains from Lebanon and Iran. Moreover, the selection pressure analysis of imp gene sequences suggested that these two AlmWB phytoplasma subpopulations had some distinct biological or ecological properties. Finally, results of the sequence and phylogenetic analyses performed on rplV‐rpsC and imp genes showed a considerably high genetic distance between AlmWB phytoplasma strains (16SrIX‐B and variants) and phytoplasmas belonging to other 16SrIX subgroups. The significance of genetic variation in phytoplasmas of 16SrIX group is discussed in relation to their biological characteristics and geographical distinction.