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.
The gene sequence data for apple mosaic virus (ApMV) in NCBI GenBank were analyzed to determine the phylogeny and population structure of the virus at a global level. The phylogenies of the movement protein (MP) and coat protein (CP) genes, encoded by RNA3, were shown to be identical and consisted of three lineages but did not closely correlate with those of P1 and P2, suggesting the presence of recombinant isolates. Recombination Detection Program (RDP v.4.56) detected significant recombination signal in the P1 region of K75R1 (KY883318) and Apple (HE574162) and the P2 region of Apple (HE574163) and CITH GD (MN822138). Observation on several diversity parameters suggested that the isolates in group 3 had higher divergence among them, compared to isolates in groups 1 and 2. The neutrality tests assigned positive values to P1, indicating that only this region experiencing balanced or contracting selection. Comparisons of the three phylogroups demonstrated high Fixation index (FST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, ±500 bp of partial MP + ‘intergenic region’ + partial CP coding regions of two Turkish isolates from apple and seven from hazelnut were sequenced and determined that their phylogenetic positions fell within group 1 and 3, respectively.
Thripsler, birçok endüstriyel üründe önemli verim kayıplarına neden olur. Bu zararlılar Türkiye'deki karantina organizmaları arasında yer aldığından, etmenlerin hızlı tespiti yeni alanlara yayılmalarını önlemek için önemlidir. Mitokondriyal sitokrom oksidaz I (COI) barkodlama geninin analizleri; moleküler yöntemlerden biri olarak Thrips teşhislerinde yaygın olarak kullanılmaktadır. Ancak COI geninin fragman uzunluğu çok kısa olduğundan, PCR sonrası agaroz jel üzerinde fragman boyutlarını ayırt etmek çok zordur. Bu çalışmada, daha önce farklı araştırmacılar tarafından kullanılan primer çiftleri kullanılarak Thrips tabaci, Frankliniella occidentalis ve F. intonsa türleri için Kapiler Jel Elektroforez (CGE) sistemi entegre edilerek yeni bir tanımlama yöntemi geliştirilmiştir. Analiz, özellikle kısa parça uzunluklu COI geninde birbirine yakın parça uzunluklarının ayrılmasında hata payını en aza indirerek, elde edilmiş güçlü sinyaller üretir. Bu sebeple, jel elektroforezi adımı ortadan kaldırılarak, tehlikeli kimyasallara maruz kalmadan güvenilir tespitler elde edildi. Yeni yöntem, tespit süresini kısalttı ve düşük DNA konsantrasyonuna sahip tek bir Thrips'in saptanmasındaki işlem hatalarınıda en aza indirdi. Bu kapiler jel elektroforezi tabanlı fragman analizi ile toplam 82 Trips bireyi (52 F. intonsa, 31 F. occidentalis) tespit edilebilmiştir. Yeni yöntem, üç farklı Thrips türünün tespiti için benzersiz, spesifik ve hızlı olarak değerlendirilmektedir. Ayrıca yakın gelecekte kısa fragman boyutlarına sahip farklı Thrips türlerinin tanımlanmasında da kullanılabileceği düşünülmektedir.
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