Fig. 4
Read-depth analyses revealed chromosomal aberrations in nwt isolates. Large CCNVs were revealed by BIC-seq analysis (upper graph for each panel) and by a read-depth analysis for heterozygous allele ratios using 10 KB long non-overlapping sliding window (lower graph). A concatenated view of the 52 largest scaffolds with a total length of 300 MB, corresponding to approximately half of the total genome of P. ramorum is shown. Scaffold numbers for large CCNV regions are indicated with pink bars, and those for LOH are shown with green bars. Scales show log (base 2) fold difference between sample isolates and reference isolates for BIC-seq analysis and log (base 2) ratios of alleles of sample isolates for the heterozygous allele frequency analysis. At each heterozygous locus, a read count ratio (more-abundant allele/less-abundant allele) was calculated. Allele count ratios larger than eight were set to eight to visualize the loss of heterozygosity. For the re-isolates Pr745#3 and Pr1156#7#1, corresponding progenitor isolates were used as reference for BIC-seq analyses (reference isolates listed in Table 3). a Pr-1556, an example of CCNV profile for the category “normal euploid”. b Nwt re-isolate Pr-745#3 from oak, an example of 3x CCNV, showing trisomy (1.5-fold increase in copy number) in the seven scaffolds. c Wt oak isolate Pr-140.9 (1x CCNV type) showing monosomy (0.5-fold decrease in copy number) in three scaffolds. d Nwt oak isolate MK516a, an example of copy number neutral LOH (2x cnLOH). Close inspection of short segments with CCNV seen as spikes in cnLOH regions (above the green bars) reveal the wt reference genome used for the BIC-seq analysis has heterozygous indels (>100 bp) in these regions. Loss of chromosomal segments harboring these indels in the nwt isolate MK516a resulted in spikes in the BIC-seq analysis. e A re-isolate from the race tube showed a mixture of nuclei with heterogeneous CCNVs. f A nwt EU1 isolate P2346 revealed extensive CCNVs and LOH when wt EU1 isolate P2363 was used as a reference