title: Estimation of the in vivo recombination rate for a plant RNA virus.
abstract: Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observations, we evaluated the in vivo recombination rate (rg) of Tobacco etch virus (TEV; genus Potyvirus, family Potyviridae) by coinfecting plants with pairs of genotypes marked with engineered restriction sites as neutral markers. The recombination rate was then estimated using two different approaches: (i) a classical approach that assumed recombination between marked genotypes can occur in the whole virus population, rendering an estimate of rg = 7.762 × 10(-8) recombination events per nucleotide site per generation, and (ii) an alternative method that assumed recombination between marked genotypes can occur only in coinfected cells, rendering a much higher estimate of rg = 3.427 × 10(-5) recombination events per nucleotide site per generation. This last estimate is similar to the TEV mutation rate, suggesting that recombination should be at least as important as point mutation in creating variability. Finally, we compared our mutation and recombination rate estimates to those reported for animal RNA viruses. Our analysis suggested that high recombination rates may be an unavoidable consequence of selection for fast replication at the cost of low fidelity.
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Tromas
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain.
authors.forename: Mark P
authors.initials: MP
authors.lastname: Zwart
authors.affiliation: Genoscreen, 1 Rue du Professeur Calmette, 59000 Lille, France.
authors.forename: Maïté
authors.initials: M
authors.lastname: Poulain
authors.affiliation: The Santa Fe Institute, Santa Fe, NM 87501, USA.|Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain.
authors.forename: Santiago F
authors.initials: SF
authors.lastname: Elena
mesh_terms: D005838:Genotype; D059645:Mutation Rate; D010935:Plant Diseases / Q000821:virology*; D017800:Potyvirus / Q000235:genetics* / Q000502:physiology; D011995:Recombination, Genetic; D014779:Virus Replication