Fig. 3

CNV of SPs reflects the phylogeny of various formae speciales and their isolates. a Heatmap illustrating the SP copy number per individual genome of various B. graminis formae speciales (avenae, dactylis, dicocci, hordei, lolii, poae, secalis, triticale and tritici) based on read mapping depth. Hierarchical clustering (Euclidean method) of the SPs and the isolates based on the CNV values is shown on the left and above the figure, respectively. Genomes belonging to the same forma specialis are color-highlighted on the left dendrogram. b Nucleotide identity matrix of high copy number SP subset (> 3 in at least one isolate, excluding BLGH_02064, BLGH_02719, BLGH_07048 due to ambiguities in the gene model) resulting by alignments with EMBOSS-Needle [106]. On the right, the highest copy number found in each forma specialis for these SPs is depicted. c Comparison between the hierarchical clustering dendrogram derived from the CNV analysis (Euclidean method) and the SNP-based UPGMA cladogram generated with SplitsTree [105] using a tanglegram generated with Dendroscope [107]. Lines connect the same isolate, while colors correspond to different formae speciales (as in A)