DYNAMIC GENOME ORGANIZATION AND GENE EVOLUTION BY POSITIVE SELECTION IN GEMINIVIRUS (GEMINIVIRIDAE)

Geminiviruses (Geminiviridae) are a diverse group of plant viruses dif fering from other known plant viruses in possessing circular, single-s tranded DNA. Current classification divides the family into three subg roups, defined in part by genome organization, insect vector, and plan t host range. Previous phylogenetic assessments of geminiviruses have used DNA and/or amino acid sequences from the replication-associated a nd coat protein genes and have relied predominantly on distance analys es. We used amino acid and DNA sequence data from the replication-asso ciated and coat protein genes from 22 geminivirus types in distance an d parsimony analyses. Although the results of our analyses largely agr ee with those reported previously, we could not always predict viral r elationships based on genome organization, plant host, or insect vecto r. Loss of correlation of these traits with phylogeny is likely due to improved sampling of geminivirus types. Unrooted parsimony trees sugg est multiple independent origins for the monopartite genome. Genome or ganization is therefore a dynamic character. Estimates of nonsynonymou s and synonymous nucleotide substitutions for extant and inferred ance stral sequences were used to evaluate hypotheses that the replication- associated and coat protein sequences evolve to accommodate plant host and insect vector specificities, respectively. Results suggest that p lant host specificity does not solely direct replication-associated pr otein evolution but that coat protein sequence does evolve in response to insect vector specificity. Genome organization and, possibly, plan t host specificity are not reliable taxonomic characters.