Exploring the genetic diversity and molecular evolution of fig badnavirus-1 from Iran

Abstract

Complete genome sequences of five fig badnavirus-1 (FBV-1) isolates from different geographic origins in Iran were obtained from infected fig plants using conventional sequencing of overlapping PCR fragment with appropriate primers. Phylogenetic analysis of these five Iranian isolates as well as the one previously sequenced USA isolate indicated that the Iranian isolates could be divided into two distinct subgroups, reflecting either divergences or two different origins. Iranian isolates were genetically distinct from the USA isolate. The phylogenetic analysis of the so-called diversity genomic region (992 nt) from 27 FBV-1 Iranian and 44 USA isolates gave two main groups. Sequences from Iran were distributed between two groups and the four subgroups of the first group besides other US isolates, and segregated according to their geographical origin. In contrast to the Iranian isolates, phylogenetic analysis grouped the USA isolates into three subgroups in the first group. To gain insight into the evolutionary forces driving the emergence of these FBV-1 populations, we analyzed the nucleotide sequences of the diversity genomic region from 71 FBV-1 isolates. Neutrality tests suggested the occurrence of purifying selection acting upon the population. For all genomic regions analyzed, diversity values were high for the nucleotide-coding sequences of the open reading frame 3, which suggests different selective constraints from the variation observed in the proteins encoded by this open reading frame. Low natural selection following founder events and rapid expansion of FBV-1 isolates into new ecological niches could result in the observed homogeneity of subpopulations.