Fig. 5: Transcriptomic and epigenomic profiles of B. duncani.

a, Logarithms of the TPM counts were used as expression values0 for each gene across the 5 chromosomes using the R package ggplot2. b, RNA-seq data as normalized heat maps across the 5 chromosomes. Chromosomes were divided into 50 kb bins and the average of the log TPM of genes within each bin was calculated. c, Relation between gene expression and distance from the centromeres to the telomeres. Chromosomes were divided into 20 bins. For each bin, the average gene expression value was plotted. Error bars denote the range of expression values within each bin for each chromosome. n = 2 biologically independent samples. d, Gene ontology (GO) enrichment of the most highly expressed genes. GO was calculated using the R package TopGO with the weight01 algorithm and the biological process tree. REVIGO was used to visualize the GO results of the most highly expressed genes (500 TPM or higher). Fisher’s exact test, one-sided, with the weight01 algorithm. e, Heterochromatin and euchromatin distribution across all five B. duncani chromosomes. Tracks correspond to H3K9me3-ChIP, H3K9ac-ChIP and IgG control and are normalized to millions of mapped reads. f, Normalized H3K9me3 counts in multigene families, and other genes encoded in the B. duncani genome (unpaired t-test with Welch’s correction, P = 0.022). n = 2 biologically independent samples. g, Comparison between epigenetic marks and gene expression. Heat maps were generated using normalized log₂ H3K9me3 and H3K9ac read counts as well as the RNA-seq TPM levels for each gene. Read counts for H3K9me3 and H3K9ac were normalized to millions of mapped reads and gene length, while TPM was determined by Stringtie. Genes were sorted from high to low TPM highlighting the correlation and anti-correlation between transcript abundance and the H3K9ac and H3K9me3 marks, respectively.