‘Candidatus Phytoplasma solani’ (Subgroup 16SrXII-A) Associated with Nicotiana tabacum Leaf Abnormality in Turkey

Year 2022, , 571 - 581, 13.09.2022

Filiz Randa Zelyüt , Adyatma Irawan Santosa , Ali Karanfil

https://doi.org/10.33462/jotaf.1028263

Cited By: 2

Abstract

Tobacco (Nicotiana tabacum) is among the agricultural products with the highest added value in Turkey. Although frequently associated with its negative effects on human health, it also provides important contributions to the Turkish economy with the employment it creates in rural areas and continues to be a strategic product. Many postgraduate theses and studies related to the sociological and economic importance of the production of this plant, which is of great importance for our country, have been carried out. However, there are very limited studies on plant diseases in tobacco production areas in Turkey. Phytoplasma is one of the important plant pathogens that cause yield loss in tobacco. Since available data on phytoplasma diseases on tobacco was very scarce worldwide, field surveys to collect samples showing phytoplasma infection-like symptoms such as yellowish color changes, leaf blisters, proliferation, dwarfism, and other physical abnormalities were carried out in Çanakkale and Balıkesir provinces of Turkey from June to August 2021. The presence of phytoplasmas in six samples was confirmed by 16S ribosomal DNA amplification by nested-PCR using universal phytoplasma primer sets, which also suggested the pathogen associated with the symptoms on tobacco. According to phylogenetic study and virtual-RFLP analysis using AluI and MseI endonuclease enzymes, the six Turkish tobacco phytoplasma strains all belong to group 16SrXII and have more than 99% nucleotide sequence identity with some members of ‘Candidatus Phytoplasma solani’ of the taxonomic subgroup ‘stolbur’ (16SrXII-A). Genetic distances analysis indicated that group 16SrI was more closely related to 16SrXII than 16SrVI, in agreement with the groups clustering in the phylogenetic tree. Neutrality tests found that 16SrI and 16SrXII groups are experiencing expanding or bottleneck selections, probably due to new mutations in the 16S rRNA gene fragment. Meanwhile, 16SrVI populations are shown to be undergoing balancing selections, indicating that its isolates have evolved for a long time.

Keywords

tobacco, phytoplasma, genetic diversity, phylogenetic, in-silico RFLP analysis

‘Candidatus Phytoplasma solani’ (Subgroup 16SrXII-A) Associated with Nicotiana tabacum Leaf Abnormality in Turkey

Abstract

Tütün (Nicotiana tabacum) Türkiye’de katma değeri en yüksek tarımsal ürünler arasında yer almaktadır. İnsan sağlığına olan olumsuz etkileri ile sıklıkla gündeme gelmesinin yanı sıra, kırsal alanlarda oluşturduğu iş gücü ile de Türk ekonomisine önemli katkılar sunmakta ve stratejik bir ürün olma özelliğini devam ettirmektedir. Ülkemiz için büyük öneme sahip bu bitkinin üretiminin sosyolojik ve ekonomik önemi ile gerçekleştirilmiş çok sayıda lisansüstü tez ve çalışma mevcuttur. Ancak, Türkiye tütün üretim alanlarında bitki hastalıkları ile ilgili olarak gerçekleştirilmiş son derece sınırlı sayıda çalışma vardır. Tütünlerde verim kaybına neden olan önemli bitki patojenlerinden bir tanesi de fitoplazmadır. Tütün fitoplazma hastalıklarına ilişkin mevcut veriler dünya çapında çok az olduğundan dolayı, Çanakkale ve Balıkesir illerinde tütün ekim alanlarında sarımsı renk değişiklikleri, yaprak kabarcıkları, proliferasyon, cücelik ve diğer fiziksel anormallikler gibi fitoplazmaların neden olduğu semptomlar gösteren örneklerin toplanması için Haziran-Ağustos 2021 tarihleri arasında Türkiye'nin Çanakkale ve Balıkesir illerinde saha araştırmaları yapılmıştır. Altı örnekte fitoplazmaların varlığı, tütün semptomlarıyla ilişkili patojeni de öneren evrensel fitoplazma primer setleri kullanılarak nested-PCR ile 16S ribozomal DNA amplifikasyonu ile doğrulanmıştır. Filogenetik analizler ve AluI ve MseI endonükleaz enzimlerini kullanılarak uygulanan sanal-RFLP analizleri bu izolatların 16SrXII ‘‘Candidatus Phytoplasma solani’’(Stolbur) grubu ve 16SrXII-A altgrubu strainleri ile %99'dan fazla nükleotid dizi özdeşliğine sahip olduğunu göstermiştir. Genetik mesafe analizi, filogenetik ağaçta kümelenen gruplarla uyumlu olarak, grup 16SrI'nin 16SrXII ile 16SrVI'dan daha yakından ilişkili olduğunu göstermiştir. Tarafsızlık testleri ile, 16SrI ve 16SrXII gruplarının, muhtemelen 16S rRNA gen fragmentinde yeni mutasyonlar nedeniyle genişleyen veya darboğaz seçimlerinden geçtiğini göstermiştir. Ayrıca, 16SrVI popülasyonlarının uzun bir süredir evrimleştiğini gösteren dengeleme seçimlerinden geçtiği gösterilmiştir.

Keywords

tütün, fitoplazma, genetik çeşitlilik, filogenetik, in-silico RFLP analizi

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