Analysis of the complete genome sequence of cucumber mosaic virus from Vinca minor and Wisteria sinensis in Iran
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Analysis of the complete genome sequence of cucumber mosaic virus from Vinca minor and Wisteria sinensis in Iran Sharifeh Dabiri 1 & Zohreh Moradi 2
&
Mohsen Mehrvar 1
&
Mohammad Zakiaghl 1
Received: 24 April 2020 / Accepted: 26 August 2020 # Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2020
Abstract We present here the first complete sequence of cucumber mosaic virus (CMV) from RNA sequencing of a dwarf periwinkle (Vinca minor) and a Wisteria sinensis in Iran by de novo assembly and annotation of contigs. The tripartite genome of CMV-IrVM and Ir-WS consists of a 3391-nucleotide (nt) RNA1, a 3038-nt RNA2, and a 2197-nt RNA3 segment. The sequence comparisons and phylogenetic analyses revealed that all three RNA segments of these two isolates belonged to the CMV subgroup II. RNA1, RNA2, and RNA3 of these two isolates, respectively shared 97.61–99.06%, 97.83–98.88%, and 97.19– 98.86% nucleotide identities to those of CMV subgroup II isolates. In genetic analysis, the 2b gene revealed more genetic variability (π = 0.2614) compared with other regions. Our results indicated that purifying selection pressure was the major force acting upon the CMV genome, although some positively selected sites were identified for all encoded proteins. Keywords Dwarf periwinkle . Wisteria . Cucumovirus . RNA-Seq . Phylogenetic analysis
Cucumber mosaic virus (genus Cucumovirus, family Bromoviridae) is present worldwide and is among the “top 10 plant viruses” due to substantial yield and economic losses (Scholthof et al. 2011). The virus can be transmitted by mechanical inoculation, and by seeds as well as by several aphid species in a non-persistent manner. The genome of cucumber mosaic virus (CMV) is composed of three positive sense, single stranded RNA segments, each separately packaged in an icosahedral/isometric capsid containing 180 coat protein subunits (Palukaitis and García-Arenal 2003). RNA1 encodes protein 1a, which is necessary for viral replication and contains helicase and methyltransferase motifs (Kadaré and Haenni 1997). RNA2 encodes protein 2a, the viral polymerase (O’Reilly and Kao 1998), as well as protein 2b, which is
Sharifeh Dabiri and Zohreh Moradi contributed equally to this work as first authors * Mohsen Mehrvar [email protected] 1
Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 91775-1163, Iran
2
Department of Plant Pathology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, P. O. BOX: 578, Sari, Iran
involved in the long-distance movement of CMV in the plant (Soards et al. 2002) and the suppression of gene silencing (Béclin et al. 1998). RNA3 encodes two proteins, the cell-tocell movement protein (protein 3a) and the coat protein (CP) (protein 3b). The CP of CMV is multifunctional and plays an important role in aphid transmission, and in viral cell-to-cell and systemic movement (Suzuki et al. 1991; Kaplan et al. 1998). CMV strains are divided into two major subgroups, I and II, with the strain
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