Fig. 4

The P. bursaria genome shows extensive copy number variation. a Scatter plot of contig length and normalized coverage of each contig. The copy numbers of contigs are highly variable in P. bursaria, but remain consistent in P. tetraurelia. The short contigs with lower coverage in P. tetraurelia are either the unassembled ends of scaffolds or AT-rich reads underrepresented in the sequencing libraries [81]. b Histogram showing the number of genes with different copy numbers in the genome. About one third of P. bursaria genes have copy numbers larger than 1.5-fold or smaller than 0.67-fold of the average copy number of the genome. Data in a and b are from Dd1. c, d Validation of gene dosage estimated from whole-genome sequencing by qPCR. Seven genes that cover the full range of copy number variation in KM2 were examined in c, and 11 genes that cover the lower end of copy number variation in Dd1 were examined in d. All values were normalized to the same internal control CDS 125F.32. Error bars represent the standard error (n ≥ 3). e Scatter plot showing that gene expression is positively correlated with gene copy number (n = 15,205). The Spearman correlation coefficient (ρ) and p value are shown