Whole genome characterization of wisteria vein mosaic virus from Iran and its relationship to other members of bean common mosaic virus group

Abstract

To date, the complete genome of two wisteria vein mosaic virus (WVMV) has been sequenced worldwide. Here, the genomic sequence of WVMV isolated from Wisteria sinensis in Iran was determined for the first time, using deep RNA sequencing and RT-PCR followed by Sanger sequencing. The sequence was 9694 nucleotides in length; excluding the 3'-poly(A) tail and contained a single open reading frame of 9279 nucleotides encoding a large polyprotein of 3092 amino acids and predicted molecular weight of 35,368 KDa. The genome contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. Sequence analysis suggested that WVMV-Ir sequence shared 76.37-86.01% nucleotide (nt) identity and 82.45-91.91% amino acid (aa) identity with two other isolates (Beijing and JEBU-p) available in the GenBank, the highest with the Chinese isolate Beijing (86.01% nt identity, 91.91% aa identity). Sequence identities over most of the genome were within the range 80-86% and 85-95% at the nt and aa levels, respectively; however, high variability was observed in the 5'-UTR (51.62%), P1 (62.03% nt identity, 50.78% aa identity) and P3 (79.82%nt identity, 78.67% aa identity) regions, suggesting that Ir, Beijing, and JEBU-p are three different strains. These variabilities may be due to different mutation phenomena of a common ancestor virus or mutations caused by different selection pressures in different agro-ecological regions. The results of the phylogenetic analysis indicated that WVMV was most closely related to soybean mosaic virus and watermelon mosaic virus and less closely related to the zantedeschia mild mosaic virus and dasheen mosaic virus. In the greenhouse, WVMV-Ir caused severe symptoms in Phaseolus vulgaris, Vicia faba, W. sinensis, Chenopodium quinoa, C. amaranticolor, and Nicotiana benthamiana.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-021-02957-8.

Keywords: Complete genome; Iran; Phylogenetic analysis; RNA-seq; Wisteria vein mosaic virus.

Fig. 1

Phylogenetic tree of the complete polyprotein amino acid sequences of WVMV and 16 other members of BCMV subgroup potyviruses, rooted with the onion yellow dwarf virus (OYDV, AJ510223). The tree was generated from a multiple sequence alignment using the maximum likelihood method in MEGAX. The significance of each branch was evaluated by constructing 1000 trees in bootstrap analysis, and the bootstrap values (≥ 70) are shown above the horizontal line at each node. This analysis involved 51 amino acid sequences. The isolate WVMV-Ir (marked) was obtained in this study. All positions containing gaps and missing data were eliminated (complete deletion option). GenBank accession numbers for viruses were shown in Table 1

Fig. 2

Maximum likelihood trees illustrating the phylogenetic relationships between the WVMV-Ir and other WVMV isolates available from the database. The phylogenetic trees were drawn from ClustalW generated multiple sequence alignments of 462 nucleotides (left) and 154 amino acids (right) of the N-terminal portion of CP gene. The isolate WVMV-Ir (marked) was obtained in this study. The sequence of OYDV (AJ510223) was used as an outgroup. Bootstrap percentages of clades, reported along the branches of the tree, derived from bootstrap-resampled data sets (1000 replications)