Molecular diversity and phylogenetic reconstruction of Pepper mild mottle virus isolates from Pakistan

Pepper mild mottle virus is a lethal Tobamovirus infecting capsicum around the globe. Molecular diversity of capsid protein gene (CP) of Pakistani Pepper mild mottle virus (PMMoV) isolates was investigated. From symptomatic pepper leaves collected from farmer’s fields, the CP gene of PMMoV RNA was amplified by specific primers designed in this study. The nucleotides sequences of Pakistani PMMoV isolates were 98.2% to 99.3% similar to each other and 97.2% to 99.3% with other isolates. Highest identities were observed with Indian (NC-3) and Chines (C27084) isolates. In phylogenetic reconstruction, Pakistani isolates grouped with Turkish and South Korean isolates. Few single nucleotide polymorphism were detected in Pakistani isolates and no insertions or deletions were observed. There was 0.0020 to 0.0063 evolutionary distance among Pakistani isolates and 0.0021 to 0.018 between Pakistani and world isolates (highest with Indian and German, and lowest with Spanish, Chines and Brazilian isolates). A frequent gene flow (Fst = 0.07103 i.e. <0.33) was observed between Pakistani and world isolates. In investigation of genetic differentiation, the figures of permutation-based statistical tests viz; Z (296.07432), Snn (0.083571) and Ks* (1.36036) were significant. In statistical analysis the values of Fu & Li’s D* and F* and Tajima’s D, were negative, exhibiting the low polymorphism frequency in studied populations.