Figure 4:

Comparative transcriptomics analyses. (A) Global DEG landscape across Bauhinia species comparisons. Pairwise comparisons include parental species (B. purpurea vs. B. variegata), hybrids (B. blakeana vs. each parent), and mid-parent value (MPV) deviation (B. blakeana vs. MPV). Arrows represent the comparisons, with the numbers and proportions of upregulated DEGs indicated at the arrow ends. Reference genome impacts are color-coded (B. purpurea: red; B. variegata: blue). (B) Reference genome bias in DEG detection between parental species. Box plots compare log2|FC| distributions (binned: 1–2, 2–4, 4–8, >8) using alternate references. Both references yield comparable total DEGs. (C) Functional divergence of species-specific upregulated genes. KEGG enrichment of B. purpurea–upregulated genes (pink) and B. variegata–upregulated genes (blue).