title: Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts.
abstract: Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Alison T M
authors.initials: ATM
authors.lastname: Lima
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Roberto R
authors.initials: RR
authors.lastname: Sobrinho
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Jorge
authors.initials: J
authors.lastname: González-Aguilera
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Carolina S
authors.initials: CS
authors.lastname: Rocha
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Sarah J C
authors.initials: SJC
authors.lastname: Silva
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: César A D
authors.initials: CAD
authors.lastname: Xavier
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: Fábio N
authors.initials: FN
authors.lastname: Silva
authors.affiliation: Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
authors.forename: Siobain
authors.initials: S
authors.lastname: Duffy
authors.affiliation: Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
authors.forename: F Murilo
authors.initials: FM
authors.lastname: Zerbini
mesh_terms: D053839:Begomovirus / Q000145:classification* / Q000235:genetics*; D001938:Brazil; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D010944:Plants / Q000821:virology*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral