Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus

Abstract

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

Molecular characterization and evolution of the resident population of some alfalfa mosaic virus (AMV) isolates in Egypt

“…The genetic diversity and molecular basis that controls AMV evolution were examined in this study using the CP gene of 42 AMV isolates. The present isolates and all other AMV strains employed in this investigation ( n = 42) had a global selection pressure dN/dS (ω) = (0.6436), indicating that the AMV CP gene is under mild purifying negative selection (evolutionary constraint), as evidenced by the dN/dS (ω) ratio < 1, similar to what has been demonstrated for other plant viruses [ 49 – 51 ]. The nucleotide diversity of all Egyptian AMV strains ( n = 15) was low (0.03787), indicating that the Egyptian AMV population was genetically stable with less variability, as reported by other authors [ 50 ].…”

“…The high frequency of AMV global distribution could be due to the wide host range of AMV and its transmission by various means, such as aphids, seeds and pollen. It has also been proposed that founder effects from plant material exchanged between various geographic regions may contribute to the genetic structure of AMV [ 51 ].…”

First report of Wisteria badnavirus 1 infecting Wisteria sinensis in Iran

“…This finding complements previous reports of viruses associated with wisteria diseases in Iran (Al‐Jaberi et al. , 2021; Moradi & Mehrvar, 2021).…”

Transmission of Alfalfa Mosaic Virus Through Subcoccinella Vigintiquatuorpunctata (L.) (Coleoptera: Coccinellidae) in Alfalfa Growing Areas in Türki̇ye

“…The RNA3 contains two ORFs encoding movement protein and coat protein (CP). (Scott et al, 1998;Moradi and Mehrvar, 2021).…”