Fig. 3

Sugarcane mosaic virus (SCMV) genome organization and mapping of de novo-assembled contigs. Labels are as in Fig. 2. a SCMV genome and polyprotein organization. Mature proteins are represented by cylinders. Coordinates are based on the Ohio isolate used as reference (JX188385.1). Every sample categorized as infected contributed one representative contig. A variable area was detected between nt 8500 and 8650. Colored arrowheads represent the location of two conserved deletions in the polyprotein coding sequence. A number 2 (group G2) indicates a 39 nt deletion (8487 to 8525) that resulted in an in-frame deletion of 13 amino acids at the C terminus of NIb. A number 3 (group G3) indicates a 45 nt deletion between nt 8487 to 8676 that resulted in a 15-amino acid deletion. In samples not marked (group G1), variation was observed without insertions or deletions. b Genome coverage after reference based assembly using Bowtie v2 for one representative sample