Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.

中文翻译：

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完整基因组分析揭示二分贝戈莫病毒的进化动力学

几个关键的进化事件标志着双生病毒的进化，最终出现了由分类为Begomovirus属的病毒所代表的分裂（二分）基因组. 该属代表了最丰富的多部分病毒组，对观察到的病毒圈中多部分物种的丰度做出了重大贡献。尽管与病毒-宿主相互作用和进化动力学相关的方面已被广泛研究，但在进化研究中很少探索这些病毒的二分性质。在这里，我们对新世界贝戈莫病毒的 DNA-A 和 DNA-B 片段进行了平行进化分析。对本研究中获得的总共 239 个全长 DNA-B 序列，结合从 GenBank 检索到的 292 个 DNA-A 和 76 个 DNA-B 序列进行了分析。结果表明，DNA-A 和 DNA-B 对进化过程的反应不同，DNA-B 比 DNA-A 更容易发生变异，也更容易重组。尽管两个片段都观察到明显的地理隔离，但也观察到 DNA-A 和 DNA-B 之间遗传结构的差异，同源片段属于不同的遗传簇。DNA-B 编码区在与 DNA-A 编码区相同的选择压力下进化。总之，我们的结果表明重配和重组之间的相互作用在不同的亚群和片段的不同水平上起作用。