Phylogenetic relationships reveal recombination among isolates of cauliflower mosaic virus

Abstract

Isolates of cauliflower mosaic virus (CaMV) differ in host range and symptomatology. Knowledge of their sequence relationships should assist in identifying nucleotide sequences responsible for isolate-specific characters. Complete nucleotide sequences of the DNAs of eight isolates of CaMV were aligned and the aligned sequences were used to analyze phylogenetic relationships by maximum likelihood, bootstrapped parsimony, and distance methods. Isolates found in North America clustered separately from those isolated from other parts of the world. Additional isolates, for which partial sequences were available, were incorporated into phylogenetic analysis of the sequences of genome segments corresponding to individual protein coding regions or the large intergenic region of CaMV DNA. The analysis revealed several instances where the position of an isolate on a tree for one coding region did not agree with the position of the isolate on the tree for the complete genome or with its position on trees for other coding regions. Examination of the distribution of shared residue types of phylogenetically informative positions in anomalous regions suggested that most of the anomalies were due to recombination events during the evolution of the isolates. Application of an algorithm that searches for segments of significant length that are identical between pairs of isolates or contain a significantly high concentration of polymorphisms suggested two additional recombination events between progenitors of the isolates studied and an event between the XinJing isolate and a CaMV not represented in the data set. An earlier phylogenetic origin for CaMV than for carnation etched ring virus, the caulimovirus used as outgroup in these analyses, was deduced from the position of the outgroup with North American isolates in some trees, but with non-North American isolates in other trees.

Evidence of Unique Genotypes of Beak and Feather Disease Virus in Southern Africa

“…Coupled to this is the risk of generating unique viruses through recombination between established virus populations and newly introduced viruses. Recombination has been well documented as a key strategy for generating diversity in both RNA and DNA viruses (2,8,21,25) and appears to contribute substantially to the level of genetic variation among BFDVs; we found evidence of recombination in all but one of the viral genomes analyzed in this study. The failure to detect any recombinant regions within the genome of the Zambian isolate taken from a wild blackcheeked lovebird further suggests that separate and unique southern African genotypes may exist.…”

Frequent occurrence of recombinant potyvirus isolates

“…We have attempted to detect recombinant isolates in several potyviruses. Our approach, inspired by that used by Chenault & Melcher (1994) on cauliflower mosaic virus, is based on the search for virus isolates showing different clustering properties in trees constructed using different short regions of their genomes. The results obtained may then be confirmed by various statistical means.…”

Possible recombination of tomato-infecting begomoviruses in Thailand

“…Previous studies of other viruses also indicate the importance of recombinations observed in these studies that were predominantly between strains of a given virus species (Chenault and Melcher 1994;Gibbs et al 1995;Lai 1992;Revers et al 1996;Roossinck 1997;Simon and Bujarski 1994).…”