Plum pox virus (PPV) strain D is globally distributed and causes serious losses in stone fruits in over 40 countries. Here, full‐length genomic sequences were analysed for 44 PPV‐D isolates from all regions of Turkey, together with partial sequences for a larger number of isolates. PPV‐D isolates from Turkey are similar to other PPV‐D isolates in all major genomic features. However, the majority of Turkish PPV‐D isolates form separate phylogenetic clusters from all other isolates and show a geographical clustering tendency, suggestive of limited movement between regions. In particular, PPV‐D isolates from Thrace and Central Anatolia formed a monophyletic sister cluster to the cluster that includes all previously known PPV‐D isolates. Two isolates with strong evidence of recombination with the PPV‐T strain were identified, together with two isolates with weaker evidence for intra‐D strain recombination. The genetic diversity of PPV‐D was found to be particularly high in Turkey (0.017 ± 0.001%), close to that observed for PPV‐D world diversity once the over‐represented isolates from Japan, the USA and Canada have been excluded (0.020 ± 0.001%). Taken together, these results suggest a long and largely isolated evolutionary history of PPV‐D in Turkey and further extend knowledge of the diversity of this highly successful strain. The high diversity of PPV‐D in Turkey, together with the basal phylogenetic position of Turkish isolates, are compatible with a hypothesis making Turkey the centre of origin of the D strain.

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Very limited information is available on the origin, diversity and evolution of Plum pox virus (PPV) 'Turkey' (T) strain. Phylogenetic analyses based on partial sequences of 421 isolates and complete genome sequences of 57 isolates, representing the geographical distribution of PPV-T in Turkey, revealed the existence of several monophyletic and, in some cases, geographically limited groups within the PPV-T strain (Ankara-Konya1-Kayseri, Ankara-Balkan, Istanbul, Konya2 and Balkan). PPV-T diversity (0.018%) was found to be greater than that of PPV strains D and Rec but lower than that of the M strain when including the newly described and divergent M-Istanbul isolates, suggesting a long evolutionary history for PPV-T. The European part of Turkey in the Balkans, close to Bulgaria where PPV was identified for the first time, appears as a likely centre of origin for PPV-T isolates. The colonization of various parts of Turkey by diverse isolates from that region, followed by secondary local spread, is the most likely scenario for the diffusion of PPV-T in Turkey.

Genotyping by sequencing (GBS), which is a highly promising technique for molecular breeding, has been implemented in apricots, including Turkish, European, and Plum Pox Virus-resistant accessions. DNA samples were digested with the ApeKI restriction enzyme to construct a genome-complexity-reduced 90-plex GBS library. After filtering the raw sequences, approximately 28 G of clean data were generated, and 17,842 high-quality single-nucleotide polymorphism (SNP) loci were discovered. A total of 561 SNP loci with 0 or 1 missing reads for the 90 accessions produced 1162 markers that were used for the cluster and population structure analysis of the same collection. The results of the SNP analysis indicated that the relation of the European accessions with the western Turkish apricots was accurately positioned. The resistant accessions from different sources were clustered together, confirming the previous finding that SEO/Harlayne-type resistance probably originated from the same source. The Malatya accessions produce most of the world's dried apricots and are likely to be a genetically distinct group. Simple sequence repeat (SSR) and self-incompatibly (SI) locus characterization of the accessions was also included. SI genotyping supported the SNP findings, demonstrating both the reliability of SNP genotyping and the usefulness of SI genotyping for understanding the history of apricot breeding. The SSR genotyping revealed a characterization similar to that of SNP genotyping with a slightly lower resolution in the dendrogram. In conclusion, the GBS approach was validated in apricots, with the discovery of a large number of SNPs, and was demonstrated to be reliable by fingerprinting the accessions in a more informative manner.

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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.

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