Determining the Evolutionary Characteristics and Genetic Structure of the Isolates of Beet Curly Top Iran Virus Based on the V2 Gene

Beet curly top Iran virus (BCTIV) is a destructive virus causing damage to agriculture industry annually. BCTIV has a circular single-stranded DNA genome with five open reading frames (ORFs): V1, V2 and V3 on genomic strand, and C1 and C2 on complementary strand. V2 acts as a suppressor of silencing interfering with this defense pathway. This study was aimed to determine the evolutionary characteristics and genetic structure of V2 among different BCTIV isolates.

Total number of 31 BCTIV V2 nucleotide sequences were extracted from the GenBank and analyzed. The nucleotide sequence was aligned and the phylogenetic tree was drawn. Nucleotide polymorphism analysis was determined. Also, the occurrence of insertion-deletion polymorphism (InDel) was investigated. Nonsynonymous (dN) and synonymous (dS) substitution rates and dN/dS ratio were calculated in order to check the selection pressure on nucleotide sequences and V2 codons. Entropy analysis was also performed to investigate possible variations in nucleotide positions.

Based on the host and geographical location, V2 sequences were placed in different clusters of the phylogenetic tree. 20 haplotypes and 94 polymorphic loci was detected. Haplotype and nucleotide diversity was calculated as 0.963 and 0.06517, respectively. The mean nucleotide differences was 23.463. InDel polymorphism was not observed. The rates of dN and dS were calculated as -0.60699 and 0.03020, respectively, both of which were not significant. The dN/dS ratio was also -20.10201. Total number of 26 positions among the codons showed a positive value of dN/dS ratio, while 34 positions had a negative value. Also, at least 9 recombination events were observed. Entropy analysis showed that nucleotide position 247 has the most changes with an entropy rate of 0.93.

The results suggest that the variation in the nucleotide sequence of BCTIV V2 can be effective in suppressing gene silencing and the pathogenicity of different isolates in different hosts. The variability of this part of the virus genome may in the future lead to an increase in the range of host range of the virus or to overcome the resistance of plant varieties.