Fig. 9
From: Protocol: rhPCR and SNaPshot assays to distinguish Plasmodiophora brassicae pathotype clusters
Example of the alignment of Plasmodiophora brassicae isolates from this study with the P. brassicae e3 reference genome [31] using the Integrated Genomics Viewer [40]. Each row represents an individual single-spore isolate, and the corresponding isolate name is displayed in the left vertical axis. The sequence of the reference genome is shown along the bottom horizontal axis. This presented region belongs to genome coordinates 43,777 to 43,816 of contig 1, and provides a clear genomic differentiation between the 5X pathotype cluster and the 3H cluster. The red boxes indicate a SNP against the reference genome, and the allelic variant in the SNP position is referred to the “Alternate” allele. Isolates of pathotype 3H belong to the alternate cluster according to this particular polymorphic region. Therefore, the other isolates containing the alternate allelic variants are grouped with pathotype 3H to form the alternate 3H cluster. Likewise, isolates of pathotype 5X belong to the reference cluster. Therefore, the other isolates containing the reference allelic variants are grouped with pathotype 5X to form the reference 5X cluster