Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey

Abstract

Plum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position 8450 up to end of genome is considered to come from PPV-M, and the remaining major genomic part is PPV-D-derived. It is regarded as third major PPV strain due to its wide distribution and prevalence in Europe. However, among over a thousand PPV isolates genetically identified in Turkey, only 10 of them (<1%) were characterized as PPV-Rec. The nearly complete genome of eight of the PPV-Rec isolates from European part of Turkey were obtained and analyzed together with PPV-Rec isolates of other countries. All major genomic features were conserved among Turkish PPV-Rec isolates. The genetic diversity of PPV-Rec isolates in Turkey (n = 8, 0.015 ± 0.001%) was found to be comparable to that observed for the isolates from eight countries (n = 10, 0.014 ± 0.001%). Particularly, genetic diversity of the minor recombinant fragment for Turkish PPV-Rec isolates was apparently higher (0.016 ± 0.001%) than the value for the 10 isolates from eight countries (0.011 ± 0.001%). The high genetic diversity was also demonstrated by high phylogenetic variation in Turkish isolates, indicating a long evolutionary history of PPV-Rec isolates in Turkey. After including Turkish isolates in the recombination analysis, the major putative recombination event of PPV-Rec isolates with a breakpoint around position 8450 was identified again, however the other recently reported putative recombination events were not supported in this study by the algorithms implemented in the RDP software.

High genetic diversity suggests a long evolutionary history of plum pox virus‐M in Turkey

“…Despite the large geographical distribution of the PPV‐M strain in Europe and the Mediterranean basin, little is known about its genomic diversity and evolutionary history. The objective of the present study was to better characterize the genetic diversity of PPV‐M in Turkey, a country considered as a hotspot of PPV diversity for at least three other strains (PPV‐T, PPV‐D and PPV‐Rec; Gürcan et al, 2020, 2021; Teber et al, 2019).…”

“…Most PPV-M outbreaks detected in Turkey have been traced back to the Bursa region, the main region of production and distribution of stone-fruit plants for planting and the main area of peach production (Gürcan, 2017). Contrary to PPV-M infections affecting mostly commercial orchards, the other three strains prevalent in Turkey, PPV-D, PPV-Rec and PPV-T, are mostly observed in residential gardens (Gürcan et al, 2020(Gürcan et al, , 2021Gürcan & Ceylan, 2016;Teber et al, 2019;Ulubaş-Serçe et al, 2009).The high diversity of PPV-D, PPV-Rec and PPV-T in Turkey, together with the fact that PPV-T is almost exclusively restricted to Turkey, argue for a long, largely isolated evolutionary history of these three strains in Turkey and is compatible with a hypothesis making this country the centre of origin of these strains (Gürcan et al, 2020;Teber et al, 2019).…”