Bolu ilinde Plum pox virus’un belirlenmesi ve kısmi moleküler karakterizasyonu

Öz

Plum pox virus (PPV), sert çekirdekli meyvelerde verim, kalite ve ekonomik kayıplara sebep olan Şarka hastalığının etmenidir. PPV, Avrupa başta olmak üzere dünya çapında tespit edilmiştir. Türkiye’de bugüne kadar yapılan çalışmalarda etmenin varlığı farklı bölgelerde sınırlı olarak tespit edilmiştir. Bolu ilinde şu ana kadar PPV’nin tespitine ilişkin herhangi bir kayıt bulunmamaktadır. Bolu ilinde 2016-2019 yılları arasında yapılan sürveyler neticesinde 306 örnek toplanmıştır. PPV’nin varlığını tespit etmek amacıyla ilk olarak DAS-ELISA ile örnekler analiz edilmiş, sadece üç adet şeftali örneğinin PPV ile enfekteli olduğu belirlenmiştir. Enfekteli örnekler daha sonra üniversal primerler (P1/P2) kullanılarak RT-PCR ile test edilmiş ve DAS-ELISA sonuçları doğrulanmıştır. Ayrıca PPV’nin ırka spesifik primerleri ile ırk düzeyinde de teşhisleri yapılmıştır. Irk düzeyinde yapılan bu teşhislerde örneklerin PPV-M (Marcus) ırkı ile enfekteli olduğu belirlenmiştir. Moleküler çalışmalar sonucunda üç izolatın kısmi kılıf protein bölgesine ait 243 nükleotidlik dizileri elde edilerek NCBI’a kaydedilmiştir. Ayrıca 38 temsili PPV sekans dizisi ile yapılan filogenetik analiz (Neighbour-Joining) sonucunda, BLAST analizinde olduğu gibi Bolu izolatlarının PPV-M izolatları ile kümelenerek diğer PPV ırklarından ayrıldığı görülmüştür. Yapılan bu çalışma ile elde edilen PPV izolatları Bolu ili için ilk kayıt niteliğindedir. Sonuç olarak, Bolu ilinde daha kapsamlı sürveylerin yapılması ve elde edilen izolatlarının tam genom dizileri elde edilerek genetik varyasyonlarının belirlenmesinin gerekliliği ortaya çıkmıştır. Enfekteli bulunan ağaçların ise tamamı imha edilmiştir.

Anahtar Kelimeler

• PPV
• şarka
• şeftali
• M ırkı
• filogenetik ağaç
• sekans

Determination and partial molecular characterization of Plum pox virus in Bolu province

Abstract

Plum pox virus (PPV), the causal agent of Sharka disease, causes yield, quality, and economic losses in stone fruits. PPV has been reported worldwide, especially in Europe. In studies to date, the presence of the virus has been identified as being restricted in different regions of Turkey. However, there is no record of PPV in Bolu province so far. Hence, surveys were carried out in Bolu province between 2016-2019, and a total of 306 samples were collected. To determine the presence of PPV, the samples were first tested by DAS-ELISA, and only three peach samples were found to be infected. DAS-ELISA results of infected samples were confirmed by RT-PCR using universal primers (P1/P2), then infected samples were identified at the strain level using strain-specific primers. The samples were found to be infected with the PPV-M (Marcus) strain and 243-bp long nucleotide sequences containing the partial coat protein gene of three isolates were deposited to NCBI. Phylogenetic analysis (Neighbor-Joining) generated by 38 representative PPV sequences indicated that Bolu isolates were clustered with PPV-M isolates and separated from other strains, as in BLAST analysis. To our knowledge, this is the first report of PPV in Bolu. This study reveals the necessity to carry out more extensive surveys to prevent the PPV dissemination in Bolu and to identify the complete genomes of the obtained isolates to determine their genetic variation. All the PPV-infected trees were destroyed as a consequence.

Keywords

• PPV
• sharka
• peach
• M strain
• phylogenetic tree
• sequence
• phylogenetic tree

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