Figure 5.

Leish Chr 31 gene expression is similar to disomic chromosomes, and the four copies appear to be down-regulated similarly. (A) Correlation between DNA AARD (x-axis) and RNA AARD (y-axis) for each SNP position in clone 3 (C3) from the tetraploid Leish Chr 31. Each dot represents one SNP position from the Leish Chr 31 in the C3 (r = 0.872, P-value = 0). On the left, a scenario in which four alleles are “A,” “C,” “C,” and “C,” and “C” is the alternate allele; therefore, WGS AARD = 0.75%. If the gene expression of all chromosome copies is silenced similarly, the AARD from the RNA-seq data for the same position would also be around 0.75 (yellow box and dot). If two chromosomal copies are silenced, this would result in “AC” with an AARD of 0.5 or “CC” with an ARDD of 1.0 (blue and green boxes and dots, respectively). (B) AARD DNA–RNA correlation plots for the Leish Chr 31 in clones C10 (r = 0.887, P-value = 0), C4 (r = 0.875, P-value = 0), C6 (r = 0.868, P-value = 0), C7 (r = 0.869, P-value = 0), C8 (r = 0.905, P-value = 0), and C9 (r = 0.866, P-value = 0). (C) DNA (red line) and RNA (blue line) AARD along Leish Chr 31 in C3. The other six clones can be seen in Supplemental Figure S9.