FIG 2.

Phase transition in C. immitis is accompanied by large changes in transcription programs and connected cis-regulatory domains. (A and B) Scatterplot and quantitative bar graph of differentially expressed (Log₂FC, >1; FDR, <0.05) nonredundant transcripts as captured by total RNA-seq (A) and csRNA-seq (B). Note the difference in scale between RNA-seq and csRNA-seq. (C) Example of a part of a connected cis-regulatory domain (20 kb) activated in spherules with novel intergenic transcription start regions (TSRs) of both stable (*) and unstable (#) transcripts. (D) Genome-wide overview of TSRs or repeats per 50 kb showing an increase in spherule-specific cis-regulatory domains in regions that lack genes in the current annotation (ASM14933v2) and often are enriched for repetitive DNA. C. immitis RS supercontig (SC) 3.1-3.6 are shown.