Constraints to genetic exchange support gene coadaptation in a tripartite RNA virus

Abstract

Genetic exchange by recombination, or reassortment of genomic segments, has been shown to be an important process in RNA virus evolution, resulting often in important phenotypic changes affecting host range and virulence. However, data from numerous systems indicate that reassortant or recombinant genotypes could be selected against in virus populations and suggest that there is coadaptation among viral genes. Little is known about the factors affecting the frequency of reassortants and recombinants along the virus life cycle. We have explored this issue by estimating the frequency of reassortant and recombinant genotypes in experimental populations of Cucumber mosaic virus derived from mixed infections with four different pairs of isolates that differed in about 12% of their nucleotide sequence. Genetic composition of progeny populations were analyzed at various steps of the virus life cycle during host colonization: infection of leaf cells, cell-to-cell movement within the inoculated leaf, encapsidation of progeny genomes, and systemic movement to upper noninoculated leaves. Results indicated that reassortant frequencies do not correspond to random expectations and that selection operates against reassortant genotypes. The intensity of selection, estimated through the use of log-linear models, increased as host colonization progressed. No recombinant was detected in any progeny. Hence, results showed the existence of constraints to genetic exchange linked to various steps of the virus life cycle, so that genotypes with heterologous gene combinations were less fit and disappeared from the population. These results contribute to explain the low frequency of recombinants and reassortants in natural populations of many viruses, in spite of high rates of genetic exchange. More generally, the present work supports the hypothesis of coadaptation of gene complexes within the viral genomes.

Figure 1. Outline of Double Inoculation Experiments with IA and IB CMV Isolates

Four IA and IB isolate combinations were inoculated in C. quinoa or in tobacco cv. Xanthi-nc. In tobacco, total RNA was extracted from inoculated (TIL) and systemic infected (TSL) leaves and encapsidated RNA was extracted from inoculated leaves (VIL). Local-lesion descendents were isolated in C. quinoa and transferred to tobacco Xanthi-nc for propagation.

Figure 2. Variation of Genotype Frequencies in Pooled Progenies from Double Inoculations of IA and IB CMV Isolates

Frequencies in TIL (black box), VIL (dark-gray box), and TSL (light-gray box) progenies are compared to those of LLH (white box) progenies. doi:10.1371/journal.ppat 0030008.g002