Occurrence and molecular characterization of a ‘Candidatus Phytoplasma omanense’-related strain associated with Prunus persica yellowing and decline in Iran

In 2014, peach (Prunus persica) yellowing and decline symptoms were observed in some fruit tree in Mehriz (Yazd province, Iran). The disease was named Mehriz peach yellowing and decline (MPYD) and characteristic symptoms were yellowing, leaf curl, witches’ broom and decline. Disease incidence was variable and up to 64% of presence was observed. Direct polymerase chain reaction was carried out on DNAs extracted from symptomatic and asymptomatic samples using using P1/P7 followed in nested PCR by R16mF2/R16mR2 and R16F2n/R16R2 to amplify the 16S ribosomal gene for phytoplasma identification. RFLP analysis of 13 amplicons with AluI, HaeIII, HhaI, HpaI, HpaII, KpnI, RsaI, MseI and Taq1 restriction enzymes showed profiles identical to those of phytoplasmas belonging to 16SrXXIX-A subgroup that is enclosing ‘Candidatus Phytoplasma omanense’. Five samples from different orchards were directly sequenced and after alignment and assembling, the resulting sequences were trimmed and compared. Since they were 100% identical to each others only one was submitted to GenBank as MPYD phytoplasma under accession no. ……………... Sequence comparison by BLAST analysis (www.ncbi.nlm.nih.gov) showed the highest sequence identity with ‘Ca. P. omanense’ classified in 16SrXXIX-A subgroup and previously associated with cassia witches’ broom in Oman. Phylogenetic analysis using neighbour-joining method (MEGA software version 7.0) confirmed that the MPYD phytoplasma is a ‘Ca. P. omanense’-related strain. Computer-simulated analysis with 17 restriction endonucleases using iPhyClassifier further confirmed that the RFLP pattern of MPYD phytoplasma 16S rRNA gene was identical (similarity coefficient 1.00) to the reference pattern of 16SrXXIX-A subgroup (GenBank accession number: EF666051) and that is therefore a member of 16SrXXIX-A subgroup. This is first report this phytoplasma in a fruit tree species in Iran and worldwide. Formerly 16SrXXIX-A and –B subgroups were detected in Cassia italica witches’ broom in Oman and Convolvulus arvensis witches’ broom in Iran respectively. This finding is enclosing the ‘Ca. P. omanense’ among phytoplasma strains infecting also fruit trees.