Figure 1 (Top left) Reconstruction of the surface structure of a cauliflower mosaic virus particle showing T=7 symmetry. (Top right) Cutaway surface reconstruction showing multilayer structure.
(From Cheng et al. (1992). Virology, 186, 655–668). (Bottom) Negative contrast electron micrograph of particles of Commelina yellow mottle virus, stained with 2% sodium phosphotungstate, pH 7.0. The bar represents 10 nm.
Figure 2 Comparison of the genome organizations of the different genera in the family Caulimoviridae. For all viruses except soybean mosaic virus (SbMV), the linearized maps begin at the 5’ nucleotide of the minus-strand primer-binding site (designated by a black diamond). For ease of comparison, the start point of the SbCMV genome is the beginning of ORF7. Light grey boxes mark open reading frames and regions within each ORF that are coloured are conserved protein domains as listed in the Pfam database (http://pfam.sanger.ac.uk/): blue is the viral movement protein domain (PF01107), corresponding to L43–E243 of the cauliflower mosaic virus (CaMV) ORF1 protein; red is the retropepsin (pepsin-like aspartic protease) domain (CD00303), corresponding to K36–Q120 of the CaMV ORF5 protein; orange is the reverse transcriptase domain (CD01647), corresponding to K273–G449 of the CaMV ORF5 protein; and yellow is the RNase H1 domain (CD06222), corresponding to I547–E673 of the CaMV ORF5 protein. Additionally, coiled-coil motifs that are characteristic of the virion-associated protein are marked purple, the conserved C-terminus of the coat protein, corresponding to L261–N429 of the CaMV ORF4 protein, is marked green, the translation transactivator active site is marked black and the position of RNA promoters is marked with an arrow.
Figure 3 Evolutionary relationships within the family Caulimoviridae based on comparison of the polymerase polyprotein gene. To obtain the nucleotide sequence alignment, amino acid sequences homologous to K36–E673 of the cauliflower mosaic virus (CaMV) P5 protein (GenBank accession NP_056728) were first aligned with ClustalX and this alignment then used to generate a DNA alignment using the program Tranalign. Poorly aligned and highly variable regions in the alignment were then removed using the program Gblocks. Maximum likelihood analysis was done using the program RAxML and the GTR+Γ model of evolution to calculate the final tree topology. The dataset was partitioned into aspartic protease, reverse transcriptase and RNase H1 domains (see Figure 2 for domain boundaries), as well as tether regions between the domains. 1000 maximum likelihood bootstrap replicates were run (bootstrap values shown in nodes of branches) using the GTR+CAT approximation of GTR+Γ. Drosophila melanogaster Gypsy virus (DmeGypV; genus Errantivirus) and Saccharomyces cerevisiae Ty3 virus (SceTy3V; genus Metavirus) were included in the analyses as outgroups. Other acronyms are ComYMV (Commelina yellow mottle virus), CsVMV (cassava vein mosaic virus), PVCV (petunia vein clearing virus), SbCMV (soybean chlorotic mottle virus), RTBV (rice tungro bacilliform virus) and TVCV (tobacco vein clearing virus).