Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175, Iran.
Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic.
Viruses. 2024 Aug 23;16(9):1351. doi: 10.3390/v16091351.
Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their "centre of emergence". We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima's D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility.
9 种豆类普通花叶病毒亚组的病毒是主要的国际作物病原体，但它们在非作物植物中亲缘关系最近的病毒大多仅在东南亚和大洋洲发现，因此该地区可能是它们的“起源中心”。我们以多种方式比较了 700 多个作物大流行和非作物病毒的完整基因组 ORF。只有三分之一的作物病毒基因组是非重组的，但超过一半的非作物病毒基因组是重组的。其中 4 种病毒来自旧大陆（非洲到东南亚）驯化的作物，另外 5 种来自新大陆作物。只有 3 个作物病毒数据集有时间信号，但它证实了所有作物病毒的最近共同祖先都在 1492 年 CE 之后跨洋海洋贸易开始之前，而所有系统发育的冠群聚类都在那之后。非作物病毒数据集的遗传多样性比作物病毒数据集的遗传多样性更高，Tajima 的 D 分析表明，它们的种群正在收缩，只有一种作物病毒的种群在扩张。dN/dS 分析表明，所有病毒的大多数基因和密码子都受到显著的负选择，而少数受到显著正选择的基因主要位于 P3 蛋白的 PIPO 编码区或 PIPO 蛋白本身。有趣的是，非作物病毒中比作物病毒中发现了更多的正选择密码子，而且，由于前者的宿主在分类学上比后者更为多样化，这可能表明正选择密码子参与了宿主范围的决定；使用 AlphaFold3 建模来研究这种可能性。
