Apricot yellows disease associated with 'Candidatus Phytoplasma phoenicium' in Iran

Almond witches’ broom (AlmWB) associated with 'Candidatus Phytoplasma phoenicium' is one of the economically important diseases of almond in Iran and Lebanon. In 2012-2015 surveys of AlmWB, apricot yellows (AprY) disease was observed in Fars province of Iran. The characteristic symptoms of the disease were leaf yellowing, inward leaf curl, scorch of leaf margins, shortened internodes, production of rosettes at the tip of branches, decline, stunting, and death. Healthy bitter almond and apricot seedlings, grafted with shoots of AprY-affected trees, exhibited phytoplasma-type symptoms. The 16S rDNA fragment F2n/R2 was amplified by nested-PCR from both AprY-affected trees and grafted seedlings. Nucleotide sequence identity, presence of species-specific signature sequences, and phylogenetic analysis of 16S rDNA allowed the assignation of detected phytoplasma strains to the species 'Ca. P. phoenicium'. In vitro and in silico RFLP analysis of the fragment F2n/R2 allowed the affiliation of AprY phytoplasma to a variant of subgroup 16SrIX-B. Within 'Ca. P. phoenicium' (16SrIX-B) population strains, identified in this and previous studies, 16 genetic lineages were determined by the combination of 19 single nucleotide polymorphisms (SNPs) identified within 16S rDNA nucleotide sequences. Interestingly, AprY phytoplasma strains belong to a unique genetic lineage distinguished by the presence of three lineage-specific SNPs. This first report of 'Ca. P. phoenicium' in association with AprY disease in Iran opens new perspectives on the epidemiology of AlmWB phytoplasma, suggesting its possible adaptation to other fruit trees