Figure 3

Copy number variation of the EnCYP51 locus. Log2 ratio plot of sequencing depth in the EnCYP51 locus of e1-101, C-strain, Lodi, and Ranch9 relative to the sequence depth in the EnCYP51 locus of Branching. CNV was confirmed in all pair-wise comparisons using CNV-seq. Depth of coverage of the EnCYP51 locus in the Branching isolate is presented as it provided the longest assembled scaffold of the locus across all isolates. Arrows and boxes depict protein coding sequences and transposable elements, respectively. Duplication boundaries upstream and downstream of the EnCYP51 coding region were common in all isolates with multiple copies of EnCYP51. Only in Lodi did an additional duplication event occur involving a shorter region of 7.4 kb. CNV-seq estimates of EnCYP51 copy numbers were validated using qPCR. Scatterplot in inset shows the correlation between CNV-seq and qPCR copy number estimates (red dashed line = linear trend line). In all isolates the duplication events did not involve the two flanking genes, En-g4918 and En-g3071, which were confirmed by qPCR to be single copy in all genomes (Figure 6D).