Distribution of RNA sequences over protein-coding and noncoding genes. (A) Read length distribution of RNA sequences mapped to the thylacine whole-genome (WG) assembly, annotated protein-coding (PC) genes (N = 19,356) and noncoding (NC) RNA genes (N = 3613). (B) Exonic enrichment and intronic depletion of RNA reads mapped to exonic and intronic regions of PC genes (at least 10% coverage) in skeletal muscle (N = 236) and skin (N = 270). Thylacine historical DNA reads mapped to the same PC genes were used as reference for comparison. (C,D) Number of RNA reads mapped to each consecutive 250-kb window genome-wide in skeletal muscle and skin, respectively. Thylacine DNA reads (SRR5055304) mapped to each consecutive 250-kb window genome-wide are in gray. (E) Venn diagram showing the top 20 genomic windows (250 kb) with the highest number of RNA reads mapped in skeletal muscle and skin. (F) Number of RNA reads mapped and coverage of each annotated PC gene (N = 19,356) in skeletal muscle. (G) Number of RNA reads mapped and coverage of each annotated PC gene (N = 19,356) in skin. (H) Venn diagram showing PC genes quantified (at least 10% coverage) in skeletal muscle and skin. (I) Number of RNA reads mapped and coverage of each annotated NC RNA gene in skeletal muscle (N = 3613). (J) Number of RNA reads mapped and coverage of each annotated NC RNA gene in skin (N = 3613). (K) Venn diagram showing NC RNA genes quantified (at least 10% coverage, N = 608 for skeletal muscle and N = 637 for skin) in skeletal muscle and skin.
