Türkiye'nin Niğde ilinde biber (Capsicum annuum L.) ile ilişkili ‘Candidatus Phytoplasma trifolii’nin (16SrVI-A) moleküler tespiti

Abstract

Türkiye'nin Niğde ili, Altunhisar ilçesindeki biber üretim alanlarında 2024 ve 2025 yıllarında yapılan saha araştırmalarında, fitoplazmalara özgü belirtiler gösteren bitkiler gözlemlenmiştir. Toplam 25 simptomatik biber örneği toplanmış ve CTAB yöntemi kullanılarak toplam nükleik asit ekstrakte edilmiştir. Örnekler, 16S rRNA gen bölgesinin PCR amplifikasyonu ile fitoplazma enfeksiyonu açısından analiz edilmiştir. Ayrıca, negatif kontrol olarak iki simptomsuz biber bitkisi de dahil edilmiştir. PCR analizleri sonucunda, simptomlu örneklerin tamamında beklenen uzunlukta amplikonlar elde edilirken, simptomsuz bitkilerde herhangi bir amplifikasyon gözlenmemiştir. Dizileme ve filogenetik analizler, tespit edilen fitoplazmanın ‘Candidatus Phytoplasma trifolii’ye karşılık gelen 16SrVI-A alt grubuna ait olduğunu ortaya koymuştur. Alt grup ataması, 16S rRNA geninin in silico (sanal) RFLP analizi ile de doğrulanmıştır. Bu çalışmada elde edilen bir izolatın temsili 16S rRNA gen dizisi GenBank veritabanına kaydedilmiştir (GenBank erişim numarası PX885052). Mevcut literatüre dayanarak, bu çalışma Türkiye'nin Niğde ilinde yetiştirilen biber bitkilerinde 'Ca. P. trifolii' enfeksiyonuna dair ilk moleküler kanıtı sunmaktadır. Bulgular, Türkiye'deki biberi enfekte eden fitoplazmaların dağılımı hakkındaki mevcut bilgilere katkıda bulunmakta ve daha fazla epidemiyolojik ve vektörle ilgili çalışmalara duyulan ihtiyacı vurgulamaktadır.

Keywords

• Candidatus Phytoplasma trifolii
• Biber
• Filogenetik analiz
• Sanal RFLP

Molecular detection of ‘Candidatus Phytoplasma trifolii’ (16SrVI-A) associated with pepper (Capsicum annuum L.) in Niğde province, Türkiye

Abstract

During field surveys conducted in 2024 and 2025 in pepper production areas in Altunhisar distinct of Niğde province, Türkiye, plants showing phytoplasma-like symptoms were observed. A total of 25 symptomatic pepper samples were collected, and total nucleic acids were extracted using the CTAB method. The samples were analyzed for phytoplasma infection by PCR amplification of the 16S rRNA gene region. In addition, two asymptomatic pepper plants were included as negative controls. PCR analysis revealed that all samples showing symptoms produced amplicons of the expected size, while no amplification was obtained from the asymptomatic plants. Sequencing and phylogenetic analyses revealed that the detected phytoplasma belonged to the 16SrVI-A subgroup, corresponding to ‘Candidatus Phytoplasma trifolii’. The subgroup assignment was further confirmed by in silico (virtual) RFLP analysis of the 16S rRNA gene. The representative 16S rRNA gene sequence of one strain obtained in this study was deposited in the GenBank database (GenBank accession number PX885052). Based on the available literature, this study provides the first molecular evidence of ‘Candidatus Phytoplasma trifolii’ infection in pepper plants grown in Niğde province, Türkiye. The findings contribute to the current knowledge on the distribution of pepper-infecting phytoplasmas in Türkiye and emphasize the need for further epidemiological and vector-related studies.

Keywords

• Candidatus Phytoplasma trifolii
• Pepper
• Phylogenetic analysis
• Virtual RFLP

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