Fig. 7

Fig. 7 Strongly reduced re-differentiation gene expression in A. mexicanus cavefish versus surface fish.

a,b, Top five enriched processes upregulated in surface fish at 7 dpci (a) and 30 dpci (b) compared to cavefish. c–f, Positive correlation of TCA/OXPHOS with Glycolysis genes at all timepoints in surface fish (c and e) but only up to 7 dpci in cavefish (d and f). g,h, Expression over time in bulk RNA-seq data. Although TCA/OXPHOS genes are initially relatively similarly expressed, they dip in cavefish at 7 dpci. From 7 dpci onwards, there is a steady increase until at least 30 dpci (g). Expression of MAS genes follows a similar pattern as TCA/OXPHOS expression (h). i,j, Significant positive correlation between the MAS and Glycolysis at late timepoints in surface fish (h) but not in cavefish (i). k–m, Expression over time in bulk RNA-seq data of two genes correlating to embcmhc expression in zebrafish, acta1 (k) and tnnc1a (l), showing strong upregulation at late timepoints in surface fish but much lower and shorter upregulation in cavefish. Mature marker myl7 expression reduces in the first days after injury, before increasing again from 7 dpci onwards (m). Selected significance is shown. n, Heatmap of sarcomere and myosin-related genes correlating to acta1, tnnc1a or myl7 in surface fish. Timepoints of interest are highlighted with black box. a,b, n = 5 biological replicates per morph per timepoint; g,h,k–m, n = 3 for uninjured cavefish and surface fish, n = 5 per morph for all other timepoints (biological replicates). a,b, Analysis performed using Metascape. c–f,i,j, Simple linear regression. g,h,k–m, Two-way ANOVA with Sidakʼs multiple test; data presented as mean ± s.e.m. pos., positively. SF, surface fish.