The Major Sources of Genetic Differentiation Among Apricot Latent Virus (ApLV) Isolates

Apricot latent virus (ApLV) is a species within Foveavirus genus (Betaflexiviridae family, Tymovirales order). Phylogenetic analyses using different ORFs nucleotide sequences divided most ApLV isolates into two clusters. However, there is little data about the sources of genetic differentiation among ApLV isolates.

Partial coat protein (CP) sequences of two Iranian ApLV isolates were determined. The complete or partial CP sequences of ApLV isolates available in the GenBank with two partial CP sequences of Iranian isolates were used for phylogenetic analyses. Also, non-overlapping regions of ORFs were considered for molecular analysis using PATRISTIC, MEGAX, and Phylip 3.67 softwares.

High nucleotide diversity 0.0 to 39.2 % was indicated for TGB2 gene, followed by CP 0.0 to 30.9 %, RdRp 0.0 to 30.3% and TGB1 0.0 to 25.9 % genes. Although Caserta12 and SB12452 isolates showed the low nucleotide diversity in RdRp, TGB1 and TGB2 genes, but high nucleotide diversity was indicated for them in CP gene (26.7 to 30.9 %). Alignment of CP indicated insertion/deletion may affect the phylogenetic differentiation of ApLV isolates. Comparision of nucleotide diversity within and between groups showing that founder effect may affect the variation of ApLV isolates. The values of FST between ApLV phylogenetic groups were < 0.33 indicating a relative rate of dissociation. Recombination breakpoints were detected in the different ORFs especially in Caserta12 isolate from Italy. The ω ratios (dNS/dS) in various proteins were conserved from 0.035 to 0.073. The ENC plot analysis indicated that the codon usage is affected by selection instead of mutation pressure for all genes except TGB2 gene. In addition, the results of mean CAI values indicated the TGB2 gene as a high expression gene. The genetic exchanges by recombination were also correlated with the appearance of new ApLV strains. ENC-Plot and mean CAI analysis are evaluated for the first time in this study to better explains the evolutionary process and fitness of ApLV.

Altogether, our analysis indicated that recombination, mutation and selection pressure are the major sources of genetic differentiation among ApLV isolates.