Fig. 4

Read-depth analyses revealed diverse chromosomal aberrations in P. ramorum from Washington State isolates. BIC-seq analysis reveals CCNVs (upper graph for each panel), while a read-depth analysis for heterozygous allele ratios (SNP ratios) detects LOH (lower graph). A concatenated view of the 31 largest scaffolds with a total length of 30 MB (c.a. half of the genome) is shown. A wild type euploid isolate ND886 was used as a reference. Scaffold numbers for large CCNV regions are indicated with pink bars, and those for cnLOH are shown with blue bars. Scales show log (base 2) fold difference between sample isolates and the reference isolate for BIC-seq analysis and log (base 2) ratios of SNP alleles of sample isolates for the heterozygous allele frequency analysis. a WSU107–0081 and b WSU107–0086 are examples of CCNV profile for the category “normal euploid”. Two wt isolates, c WSU108–0021 from Viburnum and d WSU107–0057 from Rhododendron, showed numerous CNVs in small chromosomal segments (sCNV euploid). e Wt stream isolate WSU111–0001 showed c.a. 10% reduction in copy numbers in three scaffolds 19, 27, and 28, indicating it is a heterokaryon of monosomy (1× CCNV) and euploid. f Nwt Rhododendron isolate WSU115–0118 showed slight copy number changes in numbers of scaffolds, indicating it is a mixture of monosomic nuclei. g Nwt Rhododendron isolate WSU107–0019 showed increases in SNP ratios in scaffold 7, 9, and 22 while a consistent change in chromosome copy number was not detected, which indicates cnLOH. Close inspection of short segments with CNV seen as spikes in cnLOH regions (above the blue bars) reveal the wt reference genome has heterozygous indels in these regions. Loss of chromosomal segments harboring these indels in the nwt isolate WSU107–0019 resulted in spikes in the BIC-seq analysis. h A nwt isolate WSU107–0072 revealed CCNVs and cnLOH indicating it is a heterokaryon having cnLOH and aneuploid nuclei