关键词: 番茄褪绿病毒, 贝叶斯谱系动力学, 替代速率, 时间信号, 适应性进化

Abstract:

【Objective】Tomato chlorosis virus (ToCV), a member of the genus Crinivirus in the family Closteroviridae, has emerged as one of the most prevalent viruses in tomato and other vegetable plants in China. The objectives of this study are to investigate the evolutionary history of ToCV, particularly when and where this virus was introduced into China, and to elucidate its adaptive evolutionary mechanism. 【Method】A specific primer pair flanking the coat protein gene (CP) of ToCV was designed. The CP of 13 randomly selected ToCV isolates from China was sequenced after reverse transcription and amplification using this primer pair. In addition to the novel sequence data, all published CP sequences with known sampling dates and geographic locations were obtained to assemble a total data set consisting of 103 CP sequences. A date-randomization test (DRT) was performed to assess the temporal signal in the data set and Bayesian phylodynamic framework was used to reconstruct the temporal dynamics of ToCV. Simultaneously, phylogeny-trait association analysis was used to identify whether geographic factors are involved in the adaptive evolution of ToCV. 【Result】A fragment with expected size (≈800 bp) was obtained from all the 13 ToCV-positive samples selected in this study. The CP of the 13 ToCV isolates shared more than 98% nucleotide identity with the reported sequences of other ToCV isolates. The 95% credibility intervals of rate estimate from the real sampling dates did not overlap with those from 10 replicate data sets with cluster permuted sampling date, indicating the presence of sufficient temporal signal in the sequence data allowing us to proceed with the Bayesian molecular dating analyses. Bayesian phylogenetic analyses showed that the estimated time of the most recent common ancestor of ToCV was 1920 CE (95% credibility interval 1849-1976) and the ToCV in mainland China was introduced from the USA at around 2005 CE. ToCV has been evolving at a rate of 1.12×10 ^-3 substitutions/site/year (95% credibility interval 6.08×10 ^-4-1.73×10 ^-3). This substitution rate is comparable to those estimated for animal RNA viruses, indicating that ToCV has been undergoing rapid evolutionary dynamics. In addition, significant association index, parsimony score and maximum monophyletic clade were observed when ToCV isolates were grouped by geographic origin (P<0.01), indicating a strong association between geographic factors and the adaptive evolution of ToCV. 【Conclusion】ToCV has been undergoing rapid evolutionary dynamics and its evolution was driven by geographic adaptation. These findings will be helpful in increasing our knowledge on the epidemiology of ToCV and have potential implications for developing more effective control strategies against this pathogen.

Key words: tomato chlorosis virus (ToCV), Bayesian phylodynamics, substitution rate, temporal signal, adaptive evolution