Fig. 2
Technical validation of the transcriptomic data. (a) Overview of the RNA-seq data. Raw data information (first panel), high-quality data (second panel), Q30 (third panel) and mapping ratio (fourth panel) for each RNA-seq library. (b) Distributions of the pairwise Spearman’s correlation coefficients between biological replicates (blue) and between samples from different ATs within species (red). The line in the box indicates median, the bottom and top of colored box indicates the 25th and 75th percentiles, respectively, and the whiskers extend to 1.5 IQR from the quartiles. Each box-plot is surrounded by a violin plot displaying the distribution of data. The P value was determined using a Wilcoxon rank-sum test. (c) Hierarchical clustering analysis of 107 RNA-seq samples using the expression levels of single-copy orthologous PCGs among 15 vertebrates. Average linkage hierarchical clustering was performed following Spearman’s distances between samples using the Multiple Experiment Viewer (MEV) software48. (d) Factorial map of the principal component analysis (PCA) of the expression levels of single-copy orthologous PCGs among 15 vertebrate species. The proportion of variance explained by each principal component is provided in parentheses along each axis. (e) Neighbor-joining tree based on pairwise distance matrices (1−r, r is Spearman’s correlation coefficient) between expression levels of single-copy orthologous PCGs. The scale bar indicates distances. (f) Pairwise Spearman’s correlation coefficients of expression levels of single-copy orthologous PCGs between species were plotted against the evolutionary distance. The P value was calculated using hypothesis testing.
