PCR-RFLP and sequence analysis of a non-ribosomal fragment for genetic characterization of European stone fruit yellows phytoplasmas infecting various Prunus species

Abstract

A 927 bp non-ribosomal fragment was used to assess the genetic variability of the European stone fruit yellows (ESFY) phytoplasma infecting 14 different Prunus species. For this, 175 isolates originating from four different Mediterranean countries were tested by PCR-RFLP analysis with seven restriction enzymes. No polymorphism among the ESFY phytoplasma could be observed but 12 out of 18 restriction sites differed between the homologous fragments of ESFY and apple proliferation (AP) phytoplasmas. An 846 bp fragment of a French ESFY isolate was sequenced, it included the 3′-end of a putative nitroreductase gene, an intergenic region and a truncated open reading frame. This ESFY phytoplasma sequence showed 89·7% identity with the equivalent AP phytoplasma nucleotide sequence (83·9% identity at the amino acid level). The G+C content of the entire sequence was extremely low (15·4%) and A+T-rich codons were highly preferred in codon usage. In this paper, we report the presence of the ESFY phytoplasma for the first time in Turkey and in five Prunus hosts never reported previously. Our results also indicate that the ESFY phytoplasma isolates affecting various Prunus species are genetically homogenous but can be distinguished from the AP phytoplasma. Therefore, they are likely to represent different taxons.