Ambrós Silvia, Olmo-Uceda María J, Corrêa Régis L, Elena Santiago F
Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain.
Department of Genetics, Universidade Federal do Rio de Janeiro, Rio do Janeiro, Brazil.
Evolution. 2024 Jan 4;78(1):69-85. doi: 10.1093/evolut/qpad192.
In this study, we investigated how an emerging RNA virus evolves, interacts, and adapts to populations of a novel host species with defects in epigenetically controlled plant defense mechanisms. Mutations in epigenetic regulatory pathways would exert different effects on defense-response genes but also induce large-scale alterations in cellular physiology and homeostasis. To test whether these effects condition the emergence and subsequent adaptation of a viral pathogen, we have evolved five independent lineages of a naive turnip mosaic virus (TuMV) strain in a set of Arabidopsis thaliana genotypes carrying mutations that influence important elements of two main epigenetic pathways and compare the results with those obtained for viral lineages evolved in wild-type plants. All evolved lineages showed adaptation to the lack of epigenetically regulated responses through significant increases in infectivity, virulence, and viral load although the magnitude of the improvements strongly depended on the plant genotype. In early passages, these traits evolved more rapidly, but the rate of evolution flattened out in later ones. Viral load was positively correlated with different measures of virulence, though the strength of the associations changed from the ancestral to the evolved viruses. High-throughput sequencing was used to evaluate the viral diversity of each lineage, as well as characterizing the nature of fixed mutations, evolutionary convergences, and potential targets of TuMV adaptation. Within each lineage, we observed a net increase in genome-wide genetic diversity, with some instances where nonsynonymous alleles experienced a transient rise in abundance before being displaced by the ancestral allele. In agreement with previous studies, viral VPg protein has been shown as a key player in the adaptation process, even though no obvious association between fixed alleles and host genotype was found.
在本研究中，我们调查了一种新出现的RNA病毒如何进化、相互作用并适应具有表观遗传控制的植物防御机制缺陷的新型宿主物种群体。表观遗传调控途径中的突变不仅会对防御反应基因产生不同影响，还会引起细胞生理和稳态的大规模改变。为了测试这些影响是否决定了病毒病原体的出现和后续适应性，我们在一组携带影响两条主要表观遗传途径重要元件突变的拟南芥基因型中，使一种原始芜菁花叶病毒（TuMV）株系的五个独立谱系进化，并将结果与在野生型植物中进化的病毒谱系的结果进行比较。所有进化谱系都通过感染力、毒力和病毒载量的显著增加显示出对缺乏表观遗传调控反应的适应性，尽管改善的程度强烈依赖于植物基因型。在早期传代中，这些性状进化得更快，但在后期进化速率趋于平稳。病毒载量与不同的毒力指标呈正相关，尽管从原始病毒到进化病毒的关联强度发生了变化。高通量测序用于评估每个谱系的病毒多样性，以及表征固定突变的性质、进化趋同和TuMV适应的潜在靶点。在每个谱系中，我们观察到全基因组遗传多样性的净增加，在某些情况下，非同义等位基因在被原始等位基因取代之前丰度会短暂上升。与先前的研究一致，病毒VPg蛋白已被证明是适应过程中的关键因素，尽管在固定等位基因与宿主基因型之间未发现明显关联。
