Fig. 2

Predicted, conserved protein domains (CPDs) and corresponding amino acid sequence alignments. a Linear maps (not to scale) show the three known genome arrangements for the West African cacao-infecting badnaviruses, with either four (blue), five (black), or six (green) open reading frames (ORFs), compared with cacao-infecting badnaviruses from Trinidad, Cacao mild mosaic virus (CaMMV) (gray box), and Cacao yellow-vein banding virus (CYVBV) (red box), each with four ORFs. Abbreviation with virus name: CSSV = Cacao swollen shoot virus; CSSCDV = Cacao swollen shoot CD virus; CSSTAV = Cacao swollen shoot Togo A virus; CRVV = Cacao red vein virus; DUF = domain of unknown function; Zn = zinc knuckle finger; Pepsin = pepsin-like aspartate protease; RT = reverse transcriptase; RNase H = ribonuclease H; PHD = plant homeodomain finger; and Trim = trimeric-dUTPase. b Amino acid alignment of the CPDs for four representative CSSD-badnaviral genomes from West Africa, and CaMMV and CYVBV from Trinidad. Amino acid residues that differed among most or all of the cacao-infecting badnaviral isolates are shaded. The ‘consensus’ indicates the amino acids (aa) that are 100% conserved in CPDs, across the six badnaviral species, and excludes non-conserved residues, indicated by the “–“. The black vertical bars indicate the level of aa residue conservation, ranging from 0 to 100%, for the six representative genome arrangements with CPD architecture