Esmaeilzadeh Fereshteh, Santosa Adyatma Irawan, Çelik Ali, Koolivand Davoud
Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran.
Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
Microorganisms. 2023 Sep 28;11(10):2434. doi: 10.3390/microorganisms11102434.
An analysis of the complete genome sequence of a novel isolate of tomato brown rugose fruit virus (ToBRFV) obtained from tomatoes in Iran and named ToBRFV-Ir is presented in this study. Comprehensive phylogenetic analysis utilizing key viral proteins, including 126 KDa, 183 KDa, movement protein (MP), and coat protein (CP), as well as the complete genome sequence, classified ToBRFV-Ir and 65 isolates from GenBank into three distinct clades. Notably, genetic diversity assessment revealed relatively low variability among the isolates, irrespective of their geographical or clade affiliation. Natural selection analysis based on the complete genome sequence showed that dN/dS values were consistently <1, indicating the prevailing role of negative selection across all populations. Analyses using the Recombination Detection Program and SplitsTree found no evidence of recombination events or signals in the complete genome sequence of the tested isolates. Thus, these results suggest that the genetic composition of ToBRFV remains stable without significant genetic exchange or recombination events occurring. A simple arithmetic comparison of the patristic distances and dates suggested that the time to the most recent common ancestor (TMRCA) of the ToBRFV populations is approximately 0.8 up to 2.7 with the closest tobamoviruses. An evolutionary study of the tested isolates from various countries based on the complete genome suggests Peruvian ancestry. The ToBRF-Ir isolate was successfully transmitted through mechanical inoculations to and . These findings shed light on the genetic dynamics and transmission mechanisms of ToBRFV, providing valuable insights into its molecular characteristics and potential spread among susceptible plant species.
本研究对从伊朗番茄中分离得到的一种新型番茄褐色皱纹果病毒（ToBRFV）进行了全基因组序列分析，并将其命名为ToBRFV-Ir。利用关键病毒蛋白，包括126 kDa、183 kDa、运动蛋白（MP）和外壳蛋白（CP），以及全基因组序列进行了全面的系统发育分析，将ToBRFV-Ir和来自GenBank的65个分离株分为三个不同的进化枝。值得注意的是，遗传多样性评估显示，无论分离株的地理或进化枝归属如何，其变异性相对较低。基于全基因组序列的自然选择分析表明，dN/dS值始终<1，表明负选择在所有群体中起主导作用。使用重组检测程序和分裂树进行的分析在测试分离株的全基因组序列中未发现重组事件或信号的证据。因此，这些结果表明ToBRFV的遗传组成保持稳定，没有发生重大的基因交换或重组事件。对简约距离和日期的简单算术比较表明，ToBRFV群体最近共同祖先（TMRCA）的时间与最接近的烟草花叶病毒约为0.8至2.7。基于全基因组对来自不同国家的测试分离株进行的进化研究表明其起源于秘鲁。ToBRF-Ir分离株通过机械接种成功传播到了 和 。这些发现揭示了ToBRFV的遗传动态和传播机制，为其分子特征和在易感植物物种中的潜在传播提供了有价值的见解。
