Many viral diseases threaten the sustainable production of tomato () and pepper (), which are among the most produced vegetables in the world and Türkiye. Eskişehir province of Türkiye produces a significant amount of vegetables both in the greenhouse and in the open-field. However, there have been no previous comprehensive study on the presence of viruses in tomato and pepper fields. In this study, 123 of 170 samples (72.4%) collected from tomato and pepper fields in Eskişehir in 2019 were infected with different viruses listed. While (tomato spotted wilt virus, TSWV), cucumber mosaic virus (CMV), potato virus Y (PVY), tomato mosaic virus (ToMV), tobacco mosaic virus (TMV) viruses were detected by DAS-ELISA, pepino mosaic virus (PepMV), tomato chlorosis virus (ToCV) and tobacco necrosis virus (TNV) viruses could not be detected in both host plants. To molecularly characterize the selected isolates, the complete nucleocapsid (N) gene region specific to TSWV and a partial capsid protein (CP) gene region specific to CMV were amplified via RT-PCR, followed by sequencing. Phylogenetic trees were constructed with NCBI GenBank isolates and newly sequenced isolates. Genetic structure-related analyses such as genetic diversity, genetic differentiation, gene flow, neutrality tests, selection pressure, and recombination were performed on populations. In the phylogenetic tree of the TSWV N gene, the isolates are divided into three clades of geographical origin. Genetic structure analyses revealed that TSWV populations exhibited genetic diversity. In the phylogenetic tree of the CMV CP gene, the isolates are divided into known subgroups. The analyses indicate the presence of high genetic diversity and suggest that Subgroup IB, one of the clades, may contain subgroups within itself. In addition, there are indications for the existence of different CMV subgroups in Türkiye. Although different approaches were used for both the TSWV N gene and CMV CP gene, no recombination event could be detected. This study, marking the initial identification of viruses in tomatoes and peppers within the Eskişehir region, is believed to hold substantial potential for advancing future research endeavors and enhancing disease management not only within Türkiye but also globally.

中文翻译：

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土耳其感染番茄和辣椒的番茄正孢病毒（番茄斑萎病毒）和黄瓜花叶病毒的分子特征和遗传分析

许多病毒性疾病威胁着番茄 () 和辣椒 () 的可持续生产，这两种蔬菜是世界上和土耳其产量最多的蔬菜。土耳其埃斯基谢希尔省在温室和露天田地生产大量蔬菜。然而，此前尚未对番茄和辣椒田中病毒的存在进行全面研究。在这项研究中，2019 年从埃斯基谢希尔的番茄和辣椒田采集的 170 个样本中，有 123 个样本 (72.4%) 感染了列出的不同病毒。DAS-ELISA检测到番茄斑萎病毒(TSWV)、黄瓜花叶病毒(CMV)、马铃薯Y病毒(PVY)、番茄花叶病毒(ToMV)、烟草花叶病毒(TMV)病毒、菠菜花叶病毒(PepMV) ）、番茄失绿病毒（ToCV）和烟草坏死病毒（TNV）病毒在两种寄主植物中均未检测到。为了对所选分离株进行分子表征，通过 RT-PCR 扩增了 TSWV 特异性的完整核衣壳 (N) 基因区域和 CMV 特异性的部分衣壳蛋白 (CP) 基因区域，然后进行测序。使用 NCBI GenBank 分离株和新测序的分离株构建系统发育树。对群体进行遗传结构相关分析，如遗传多样性、遗传分化、基因流、中性测试、选择压力和重组。在 TSWV N 基因的系统发育树中，分离株根据地理起源分为三个分支。遗传结构分析表明，TSWV 群体表现出遗传多样性。在 CMV CP 基因的系统发育树中，分离株被分为已知的亚组。分析表明存在高度遗传多样性，并表明分支之一的 IB 亚群本身可能包含亚群。此外，有迹象表明土耳其存在不同的 CMV 亚群。尽管对 TSWV N 基因和 CMV CP 基因使用了不同的方法，但没有检测到重组事件。这项研究标志着埃斯基谢希尔地区西红柿和辣椒中病毒的初步鉴定，据信不仅在土耳其国内而且在全球范围内，对于推进未来的研究工作和加强疾病管理具有巨大的潜力。