Molecular Population Genetics of Cucumber Mosaic Virus in California: Evidence for Founder Effects and Reassortment

Abstract

The structure and genetic diversity of a California Cucumber mosaic virus (CMV) population was assessed by single-strand conformation polymorphism and nucleotide sequence analyses of genomic regions 2b, CP, MP, and the 3 nontranslated region of RNA3. The California CMV population exhibited low genetic diversity and was composed of one to three predominant haplotypes and a large number of minor haplotypes for specific genomic regions. Extremely low diversity and close evolutionary relationships among isolates in a subpopulation suggested that founder effects might play a role in shaping the genetic structure. Phylogenetic analysis indicated a naturally occurring reassortant between subgroup IA and IB isolates and potential reassortants between subgroup IA isolates, suggesting that genetic exchange by reassortment contributed to the evolution of the California CMV population. Analysis of various population genetics parameters and distribution of synonymous and nonsynonymous mutations revealed that different coding regions and even different parts of coding regions were under different evolutionary constraints, including a short region of the 2b gene for which evidence suggests possible positive selection.RNA viruses are intrinsically heterogeneous, partly because of the error-prone nature of RNA replication (14,20). In addition, genetic exchange (either by recombination or by reassortment) can be another major evolutionary force which is able to rapidly increase variation and is proposed to have evolved to offset fitness losses due to the accumulation of deleterious mutations through the effect known as Muller's ratchet (6). Other evolutionary factors such as selection, genetic drift, and bottleneck effects can serve to decrease diversity. However, in spite of the high potential for variability of RNA viruses, most RNA virus populations analyzed so far are genetically stable with relatively low diversity (17).Cucumber mosaic virus (CMV) is a tripartite, positive-sense plant RNA virus (Fig. 1). CMV occurs naturally worldwide and has perhaps the widest host range among all plant viruses, including some monocotyledonous and a great number of dicotyledonous plant hosts (26). RNA1 encodes the 1a protein, which together with the RNA2-encoded 2a protein forms the viral component of the replicase complex (19). RNA2 also encodes a second protein, 2b. The 2b coding region overlaps the coding region for the C-terminal portion of the 2a protein but is in a different reading frame register. The CMV 2b protein functions in host-specific long-distance movement (12, 13) and as a virulence determinant by suppressing posttranscriptional gene silencing (3). RNA3 encodes two proteins. The 3a protein is a cell-to-cell movement protein (MP), and the 3b protein is the capsid protein (CP), which is also involved in cell-to-cell movement and aphid-mediated CMV transmission from plant to plant (5, 27, 28). (16), and nucleotide sequence analysis (8,9,33,34,39). Most of these studies were phylogenetically oriented and allowed the subdivisio...

Evolution and structure of Tomato spotted wilt virus populations: evidence of extensive reassortment and insights into emergence processes

“…3). showed that reassortment occurs at rather low rates in viruses of the family Bunyaviridae (Henderson et al, 1995;Nemirov et al, 1999) or of other families (Fraile et al, 1997;Lin et al, 2004;Roossinck, 2002;Bonnet et al, 2005;Miranda et al, 2000;Iturriza-Gó mara et al, 2001;Watanabe et al, 2001;McDonald et al, 2009), which could be due to strong selection acting against reassortants (Brown et al, 2002;Fraile et al, 1997;Escriu et al, 2007). Some viral taxa seem however to show more extensive reassortment (Silander et al, 2005;Lindstrom et al, 2004;Nelson et al, 2008;Khiabanian et al, 2009).…”

Bioassay and phylogeny of five Iranian isolates of Cucumber mosaic virus from different hosts based on CP gene sequence

“…Of interest it is also that, among our five isolates, Ab (originated from weed A. theophrasti) showed the highest nucleotide sequence variation in comparison with other isolates. Based on our results, there was no correlation between CP gene sequence variation and geographical origin or original host plant, as described before (Hayakawa et al 1989;Lin et al 2004). To our knowledge, this is the first report of CMV infection of A. theophrasti in the world.…”

“…Coat protein gene of CMV isolates was amplified by immunocapture RT-PCR protocol (Nolasco et al 1993), using F4 (forward) 5'-TTGAGTCGAGTCATG-GACAAATC-3'/F3 (reverse) 5'-AACACGGAATCA-GACTGGGAG-3' primer pair designed by Lin et al (2004). Briefly, fresh leaf tissue of N. tabacum plant, infected with each CMV isolate, was macerated in PBST buffer containing 2% PVP and incubated overnight at 4°C in PCR vials which had been coated with CMV IgG before.…”

Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies

“…It has been shown that selection against heterologous gen combinations increases as host colonization progresses along the infection cycle of Cucumber mosaic virus [32], affecting the frequency of genetic exchange. This explains that recombinants and reassortants are often found at low frequencies [33,34], although the frequency of particular combinations may be dependent on agro-ecological factors [17,19], and support the hypothesis of co-adaptation of gene complexes within the viral genomes [32,35].…”