Phylogenetic and Population Analysis of Lettuce mosaic virus Isolates Based on the Coat Protein Gene

Abstract

Lettuce mosaic virus (LMV) is one of the most important and destructive members of Potyviruses in the family Potyviridae that is transmitted by aphid and seed which cause economic damage and serious yield losses to different crops around the world. To explore phylogenetic relationships, population evolution, and the effect of selection forces on the complete coat protein (CP) gene of LMV isolates, 36 complete coat protein gene sequences retrieved from the GenBank database in several different countries in four continents: Central and East Asia (China, Taiwan, South Korea, and Turkey), Europe (France), Africa (Tunisia), and America (Chile and Brazil). The phylogenetic tree of LMV isolates was grouped into independent clades with the significance of FST values (>0.27). The ratio of dN/dS is calculated less than one and showed that the LMV-CP has been under negative selection. Statistical tests (Tajima’s D, Fu and Li’s D* and F*) were used to estimate non-significantly negative values for all clades and geographic populations except for the Brazilian population and Clade III in a phylogenetic group. The negatives values revealed that there is less polymorphism estimation. All geographic populations in four phylogroups of LMV seem to be at equilibrium because all neutrality test statistics were non-significant. The findings suggested that the dynamics of LMV molecular evolution may be dependent on mutation, recombination, and negative selection. No recombination events were observed in this part of the LMV genome. Therefore, this study provides the first time evolution and differentiation between populations of LMV isolates from around the world and suggested that they may be occurred by the transmission of the virus among lettuce plants by types of aphid species, migration in different geographical areas by infected seeds and plant material, and broad host range which seems that these events have played an important role in shaping the LMV population structure.