title: Both point mutation and RNA recombination contribute to the sequence diversity of citrus viroid III.
abstract: Field-grown citrus trees often harbor complex mixtures of 4-5 different viroid species, and the presence of citrus viroid III (CVd-III) has been shown to reduce the rate of tree growth without inducing disease. To more fully define the structure of its quasi-species, we have examined nine citrus viroid complexes for the presence of previously undescribed sequence variants of CVd-III. Analysis of 86 full-length cDNAs generated from these nine viroid complexes by RT-PCR revealed the presence of 20 new CVd-III variants. Chain lengths ranged from 293-297 nucleotides, and sequence changes were confined largely to the lower portions of the central conserved region and variable domain. The previously described variants CVd-IIIa (297 nt) and CVd-IIIb (294 nt) were clearly predominant, but phylogenetic analysis indicated that certain isolates may contain representatives of two additional fitness peaks. At least one group of CVd-III variants appears to have arisen as a result of RNA recombination. Populations recovered from diseased/declining trees were the most diverse, but even dwarfing isolates originating from old line Shamouti trees showed considerable variability.
authors.affiliation: Molecular Plant Pathology, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA. rowens@asrr.arsusda.gov
authors.forename: R A
authors.initials: RA
authors.lastname: Owens
authors.forename: G
authors.initials: G
authors.lastname: Yang
authors.forename: D
authors.initials: D
authors.lastname: Gundersen-Rindal
authors.forename: R W
authors.initials: RW
authors.lastname: Hammond
authors.forename: T
authors.initials: T
authors.lastname: Candresse
authors.forename: M
authors.initials: M
authors.lastname: Bar-Joseph
mesh_terms: D001483:Base Sequence; D002957:Citrus / Q000821:virology*; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D017354:Point Mutation; D012367:RNA, Viral / Q000032:analysis; D011995:Recombination, Genetic; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D014772:Viroids / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D012367:RNA, Viral