Detection and genetic variation analysis of apple chlorotic leaf spot virus and apple stem grooving virus in wild apple (Malus sieversii) from Xinjiang, China

Here, we produced nucleotide and amino acid sequences of the movement protein (MP) and the coat protein (CP) genes of apple chlorotic leaf spot virus (ACLSV) and apple stem grooving virus (ASGV) from wild apple of Xinjiang, the main progenitor of the domesticated apple. Genetic variation and phylogenetics were assessed using these and previously reported sequences. Phylogenetic analysis of ACLSV nucleotide and amino acid data sets assigned some ACLSV variants to known groups and others to novel clades. In an MP-based phylogenetic tree, ASGV sequences downloaded from GenBank and those of wild apple isolates were assigned to separate groups. A recombinant sequence was identified in a ACLSV variant (MS-GL-1-c-3) of wild apple, and both parents of the recombinant had been isolated from the same plant (GL). Two potential recombination events of ASGV (MS-GL-2-g-3 and MS-NF-1-g-3) were identified in this study. These findings may constitute a valuable basis for future studies on variability of virus genetics and pathogenicity.

Automated summary

This study analyzed the genetic variation and phylogenetics of apple chlorotic leaf spot virus (ACLSV) and apple stem grooving virus (ASGV) using nucleotide and amino acid sequences from wild apple. The results identified known groups and novel clades within ACLSV, as well as separate groups within ASGV. Recombinant sequences were also identified in ACLSV and potential recombination events were found in ASGV. These findings provide valuable insights into the variability of virus genetics and pathogenicity.