Supplementary Table 1. Predicted genes of C49A.
Gene
CP
V2
Rep
TrAP
Ren
C4
Coordinates
278-1048
118-474
2588-1497
1600-1481
1455-1051
2674-2129
Predicted coding capacity (no.
of amino acids/mol. wt. [kDa])
256/29.6
118/13.7
363/40.8
39/4.6
134/15.6
181/20.5
Supplementary Fig. 1 Neigbour-joining phylogenetic dendrograms based upon alignments
of C49A with the complete nucleotide sequences of selected begomovirus genomes (or DNA
A components) available in the databases (A) and C49β with the complete nucleotide
sequences of selected betasatellites (B). The numbers at nodes represent percentage bootstrap
confidence scores (1000 replicates). The dendrograms were arbitrarily rooted on the
sequences of Cotton leaf crumple virus (AF4809402) and Croton yellow vein mosaic
alphasatellite (FN658710), respectively, as outgroups. The viruses used are Cotton leaf curl
Alabad virus (CLCuAlV), Cotton leaf curl Banglore virus (CLCuBaV), Cotton leaf curl
Burewala virus (CLCuBuV), Cotton leaf curl Gezira virus (CLCuGeV ), Cotton leaf curl
Kokhran virus (CLCuKoV), Cotton leaf curl Multan virus (CLCuMuV), Cotton leaf curl
Rajastan virus (CLCuRaV), Cotton leaf curl Shadadpur virus (CLCuShV), Papaya leaf curl
virus (PaLCuV ), Gossypium punctatum mild leaf curl virus (GPMLCuV) and Tomato leaf
curl Karnataka virus (ToLCuKV ), whereas the betasatellites used are Ageratum leaf curl
betasatellite
(ALCuB), Chilli leaf curl betasatellite (ChLCuB), Cotton leaf curl Gezira
betasatellite (CLCuGeB), Cotton leaf curl Multan betasatellite (CLCuMuB), Papaya leaf curl
betasatellite (PaLCuB), Tobacco leaf curl betasatellite (TbLCuB), Tomato yellow leaf curl
betasatellite (ToYLCuB), Tomato yellow leaf curl China betasatellite (ToYLCuCNB) and
Tomato yellow leaf curl Thailand betasatellite (ToYLCuThB). In each case the database
accession number is given.
Supplementary Fig. 2 Sequence of C49A surrounding the overlap of the Rep, TrAP and
REn genes highlighting coding sequences, start and stop codons (as indicated by the key at
the top). Note the truncated (predicted 39 amino acid coding capacity) TrAP gene.