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

Background and aims: apricot latent virus (aplv) is a species within foveavirus genus(betaflexiviridae family, tymovirales order). phylogenetic analyses using different orfsnucleotide sequences divided most aplv isolates into two clusters. however, there is littledata about the sources of genetic differentiation among aplv isolates.materials and methods: partial coat protein (cp) sequences of two iranian aplv isolateswere determined. the complete or partial cp sequences of aplv isolates available in thegenbank with two partial cp sequences of iranian isolates were used for phylogeneticanalyses. also, non-overlapping regions of orfs were considered for molecular analysisusing patristic, megax, and phylip 3.67 softwares.results: high nucleotide diversity 0.0 to 39.2 % was observed for tgb2 gene, followed bycp 0.0 to 30.9 %, rdrp 0.0 to 30.3% and tgb1 0.0 to 25.9 % genes. although caserta12and sb12452 isolates showed the low nucleotide diversity in rdrp, tgb1 and tgb2 genes,but high nucleotide diversity was detected for them in cp gene (26.7 to 30.9 %). alignmentof cp indicated insertion/deletion may affect the phylogenetic differentiation of aplvisolates. comparision of nucleotide diversity within and between groups showing thatfounder effect may affect the variation of aplv isolates. the values of fst between aplvphylogenetic groups were < 0.33 indicating a relative rate of dissociation. recombinationbreakpoints 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 plotanalysis indicated that the codon usage is affected by selection instead of mutation pressurefor all genes except tgb2 gene. in addition, the results of mean cai values indicated thetgb2 gene as a high expression gene. the genetic exchanges by recombination were alsocorrelated with the appearance of new aplv strains. enc-plot and mean cai analysis areevaluated for the first time in this study to better explains the evolutionary process and fitnessof aplv.conclusion: altogether, our analysis indicated that recombination, mutation and selectionpressure are the major sources of genetic differentiation among aplv isolates.