Fig 1.
General features of the C4/AC4 protein encoded by geminiviruses.
(A) Genome organization of geminiviruses. (B) Features of selected C4/AC4 proteins. Protein size in aa is indicated on the right. The cTP was predicted by ChloroP (http://www.cbs.dtu.dk/services/ChloroP/) [72]. The N-terminal myr site and the pal site were predicted by GPS-Lipid (http://lipid.biocuckoo.org/webserver.php) [73]. For further information, see S1 and S2 Tables. cTP, predicted chloroplast transit peptide; myr, predicted myristoylation site; pal, predicted palmitoylation site.
Table 1.
Features of the C4 proteins encoded by the type species of the different Geminivirus genera.
Table 2.
Described plant interactors of C4/AC4 proteins.
Fig 2.
Phylogenetic tree of C4/AC4 proteins and presence/absence of predicted cTP and myr/pal sites.
Annotated C4/AC4 proteins were used in (A); in (B), potential proteins encoded by predicted ORFs with positional and sequence homology to C4 (predicted C4; dark blue) as well as Capulavirus, Grablovirus, and Topilevirus C3 proteins (pink) are included. In light blue, annotated C4/AC4 proteins. The presence or absence of predicted cTP, myr, and pal is indicated; protein size in aa is shown on the right. Numbers within the gray boxes correspond to different Geminivirus genera as follows: 1, Becurtovirus; 2, Begomovirus (BGYMV: NW; TYLCV: OW); 3, Capulavirus; 4, Curtovirus; 5, Grablovirus; 6, Maldovirus; 7, Mastrevirus; 9, Opunvirus; 10, Topilevirus; 11, Topocuvirus; and 12, Turncurtovirus. The gray boxes without name correspond to unclassified viruses. For further information, see S1 and S2 Tables. cTP, predicted chloroplast transit peptide; myr, predicted myristoylation site; ORF, open reading frame; OW, Old World; NW, New World; pal, predicted palmitoylation site.
Table 3.
Nonsynonymous to synonymous substitution ratios (dN/dS) calculated for OW and NW begomoviruses.