Orthologous oscillatory genes between P. pacificus and C. elegans. (A) A total of 6594 one-to-one orthologous gene pairs were identified between P. pacificus and C. elegans. In P. pacificus, the oscillating gene set contains 1002 one-to-one orthologous genes; in C. elegans, it includes 1285 one-to-one orthologous genes. Of these genes, 528 one-to-one orthologous genes are oscillating in both species (defined as P. pacificus conserved oscillations; PCO), 474 orthologous genes show a P. pacificus–specific oscillating pattern (PSO), and 757 orthologous genes were classified as C. elegans–specific oscillations (CSO). (B) The heatmaps show the developmental expression of the three gene classes (PCO, PSO, and CSO) in P. pacificus and C. elegans. (C) The matrices show the levels of significance for the tests of protein domain overrepresentation among the three oscillating gene classes. The color scale indicates the fold change; the labeling of matrix cells shows the number of oscillating genes containing a specific protein domain. (D) The box plots display the variation in the amplitude of oscillation between PCO and PSO in P. pacificus (red) and between PCO and CSO in C. elegans (blue). The bar plots show the distribution of genes with five different amplitude classes among top 11 protein domains highly enriched in PCO.
