Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus

Abstract

An analysis of nucleotide sequences in five coding and one non-coding genomic regions of 35 Cucurbit yellow stunting disorder virus (CYSDV) isolates collected on a local scale over an 8 year period is reported here. In total, 2277 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Mean nucleotide diversity for the whole population in synonymous positions in the coding regions was 0?00068, whilst in the 59 untranslated region (59 UTR) of genomic RNA2, it was 0?00074; both of these values are very small, compared with estimates of nucleotide diversity for populations of other plant viruses. Nucleotide diversity was also determined independently for each of the ORFs and for the 59 UTR of RNA2; the data showed that variability is not distributed evenly among the different regions of the viral genome, with the coat protein gene showing more diversity than the other four coding regions that were analysed. However, the low variability found precluded any inference of selection differences among gene regions. On the other hand, no evidence of selection associated with host adaptation was found. In contrast, at least a single amino acid change in the coat protein appears to have been selected with time. INTRODUCTIONRNA viruses are known to have a high variation potential, because of their high mutation and recombination rates (Drake & Holland, 1999;Bruyere et al., 2000;Malpica et al., 2002). However, this mutability does not necessarily result in a high degree of genetic variability of their populations, as the genetic composition of virus populations will depend on evolutionary forces, such as selection and random genetic drift. In fact, for most of the cases analysed, plant virus populations have been shown to be genetically stable (reviewed by García-Arenal et al., 2001). To explain this stability, population bottlenecks associated with ecological factors, such as colonization of new hosts or new geographical areas, are often invoked (Fraile et al., 1996(Fraile et al., , 1997a Sánchez-Campos et al., 2002). Also, selection pressures, including the maintenance of structural features of the virus or interaction with host and vector factors, may contribute to genetic stability (e.g. Moreno et al., 2004) (reviewed by García-Arenal et al., 2001). The relative contribution of these evolutionary forces can be studied by analysing the genetic structure of plant virus populations. Analysis through temporal series might be particularly informative, although studies of this type are scarce (Fraile et al., 1997b; Sánchez-Campos et al., 2002).We report here a local-scale analysis of the genetic diversity of a natural population of Cucurbit yellow stunting disorder virus (CYSDV), a whitefly-transmitted closterovirus that affects cucurbit crops extensively in many warm and temperate areas of production (Hassan & Duffus, 1991; Célix et al., 1996;Wisler et al., 1998; Abou-Jawdah et al., 2000;Desbiez et al., 2000;Kao et al., 2000;Louro et al., 2000). Whitefly-transmitted closteroviruses are respo...

The Rate and Spectrum of Spontaneous Mutations in a Plant RNA Virus

“…This agreement suggests that plant RNA viruses have lower mutation rates than those of their animal counterparts. Indeed, this difference in mutation rates may help to partially explain why the rates of molecular evolution of most RNA plant viruses are apparently lower than those observed for RNA animal viruses (Rodríguez-Cerezo et al 1991;Fraile et al 1997;Marco and Aranda 2005;Herránz et al 2008). This difference between animal and plant RNA viruses raises an intriguing question: Given that plant and animal RNA viruses do not form separated phylogenetic groups and that they are replicated by similar polymerases, why do plant RNA viruses show lower mutation rates?…”

“…In the case of plant RNA viruses, it has been repeatedly reported that their populations are highly genetically stable (Rodríguez-Cerezo et al 1991;Fraile et al 1997;Marco and Aranda 2005;Herránz et al 2008) in comparison with their animal counterparts, although reports of higher substitution rates also exist (Fargette et al 2008;Gibbs et al 2008). This peculiar behavior might be due in part to stronger stabilizing selection, weaker immune-mediated positive selection (García-Arenal et al 2001), the existence of strong bottlenecks during cell-to-cell movement and systemic colonization of distal tissues (Hall et al 2001;Sacristán et al 2003;Li and Roossinck 2004), severe bottlenecks during vector-mediated transmission (Ali et al 2006;Moury et al 2007;Betancourt et al 2008), or differences in the replication mode compared to lytic animal viruses (French and Stenger 2003;Sardanyés et al 2009).…”

Whitefly-transmitted criniviruses of cucurbits: current status and future prospects

“…Early studies based on single-strand conformational polymorphism (SSCP) and sequencing of the Hsp70h and CP gene of CYSDV isolates from different geographical areas showed slightly distinct CP and Hsp70h patterns [51,72,73,80]. Hsp70h-based analysis showed that CYSDV population in the same plant was closely related but had one predominant variant independent of the host [73].…”

“…Five coding and one non-coding genomic regions of a CYSDV population were examined in different cucurbit hosts in Spain [51]. CYSDV showed high genetic stability with negligible nucleotide diversity over a period of 8 years regardless of the genomic region or host [51]. Exceptionally, the low genetic variability resulted in positive selection of an amino acid in the CP [51].…”

“…Thus, CYSDV could be divided into two divergent subpopulations: a 'western' (isolates from Jordan, Lebanon, North America, Spain, France, Tunisia, Greece and Turkey) and an 'eastern' subpopulation (isolates form Saudi Arabia and Iran) [12,72,73,80,95]. Five coding and one non-coding genomic regions of a CYSDV population were examined in different cucurbit hosts in Spain [51]. CYSDV showed high genetic stability with negligible nucleotide diversity over a period of 8 years regardless of the genomic region or host [51].…”