title: 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.
authors.affiliation: Department of Plant Pathology, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, USA.
authors.forename: Han-Xin
authors.initials: HX
authors.lastname: Lin
authors.forename: Luis
authors.initials: L
authors.lastname: Rubio
authors.forename: Ashleigh B
authors.initials: AB
authors.lastname: Smythe
authors.forename: Bryce W
authors.initials: BW
authors.lastname: Falk
mesh_terms: D002140:California; D017799:Cucumovirus / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D018703:Founder Effect; D014644:Genetic Variation; D009154:Mutation; D010802:Phylogeny; D018807:Polymorphism, Single-Stranded Conformational; D011995:Recombination, Genetic; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins