Evolutionary Dynamics and Population Genetics of Ash Shoestring-Associated Virus in a European-Wide Survey

Ash shoestring-associated virus (ASaV; Emaravirus fraxini ) is a five-segmented, negative-sense RNA virus associated with chlorosis and leaf deformation in Fraxinus species. This study investigated the genetic diversity and evolutionary dynamics of ASaV by analyzing nearly full-length RNA2–RNA5 and partial RNA1 sequences from isolates collected from different geographic regions and Fraxinus hosts. The sequence data uncovered that ASaV has a conserved genome, in which RNA3 and RNA5 showed more genetic divergence than other segments in the sequenced isolates. ASaV RNA3 and partial RNA1 were the most informative genomic regions for phylogenetic studies. There was a correlation between the clustering of the ASaV isolates and host species when the phylogenetic tree was constructed based on the RNA1 region. The ASaV genome is predominantly under purifying selection. Newly designed primers in this study facilitated robust amplification of genomic regions.