Fig. 2.

Maize chlorotic mottle virus (MCMV) genome organization and alignment of de novo-assembled contigs. Symptomatic (S) and asymptomatic (A) maize, cultivated (*) or wild (**) sorghum, or napier grass (***) were sampled. The county of origin is indicated after the sample number and symptoms. a MCMV genome organization. Coordinates are based on reference sequence number X14736.2. Open reading frames are represented by cylinders. Genomic RNA is represented by a solid line. Arrow heads mark the leaking termination codon in p50 and in p7. Red and black lines, to scale, represent contigs of positive or negative polarity, respectively, aligned to the reference. For every sample categorized as infected the longest contig is shown. Shorter, redundant contigs were not illustrated. Contig size, alignment size, and similarity (%) are indicated. b Genome coverage after reference based assembly using Bowtie v2 for one representative sample. Sequence depth is indicated on the left. GC content is color coded