Biological properties, genetic structure and molecular variability of brome mosaic virus population

Abstract Brome mosaic virus (BMV) is a member of the Bromovirus genus in the Bromoviridae family. Due to its genetic and biochemical features, BMV is considered as one of the most important plant viruses in molecular plant pathology. Although BMV is widely used in many laboratories as a convenient model for molecular studies, knowledge regarding its biology, pathogenicity, virulence and genetic differentiation within natural populations is rather limited. In this study, the complete genome sequence of 16 BMV isolates originating from different hosts was obtained. Recombination, selection pressure and phylogenetic analyses were carried out using newly obtained BMV sequences and 10 others described to date. The nucleotide and amino acid sequence identities of the 26 BMV sequences were relatively high and ranged from 96.4% to 99.4% for nucleotide sequences and from 95.7% to 99.6% for amino acid sequences. Further analysis revealed that both selection and recombination are shaping the population structure of BMV. The presence of six possible recombination sites within open reading frames and one within the 3′ untranslated region of RNA2 was identified. Selection pressure analysis indicated that most codons were subjected to purifying selection; however, 14 codons were found to be under positive selection pressure. The results presented here expand the current knowledge regarding BMV diversity and the evolutionary forces shaping BMV population structure.