PHYLOGENETIC-RELATIONSHIPS REVEAL RECOMBINATION AMONG ISOLATES OF CAULIFLOWER MOSAIC-VIRUS

Isolates of cauliflower mosaic virus (CaMV) differ in host range and s ymptomatology. Knowledge of their sequence relationships should assist in identifying nucleotide sequences responsible for isolate-specific characters. Complete nucleotide sequences of the DNAs of eight isolate s of CaMV were aligned and the aligned sequences were used to analyze phylogenetic relationships by maximum likelihood, bootstrapped parsimo ny, and distance methods. Isolates found in North America clustered se parately from those isolated from other parts of the world. Additional isolates, for which partial sequences were available, were incorporat ed into phylogenetic analysis of the sequences of genome segments corr esponding 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 o r with its position on trees for other coding regions. Examination of the distribution of shared residue types of phylogenetically informati ve 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 significan t length that are identical between pairs of isolates or contain a sig nificantly high concentration of polymorphisms suggested two additiona l recombination events between progenitors of the isolates studied and an event between the XinJing isolate and a CaMV not represented in th e data set. An earlier phylogenetic origin for CaMV than for carnation etched ring virns, the caulimovinrs used as outgroup in these analyse s, was deduced from the position of the outgroup with North American i solates in some trees, but with non-North American isolates in other t rees.