Figure 1

Genome-wide analysis of protein-coding genes in N. coriiceps. (A) Venn diagram displaying the overlap in gene families in six fish species. A total of 18,131 gene families that are included in gray background were used to analyze gain and loss of gene in six fish. (B) Lineage-specific genes expansion and contraction among six fish. The numbers in boxes are identifiers for internal branches of the phylogeny. Numbers on each branch denote the number of gene gains (+)/losses (-). AE and AR denote average expansion family (mean number of genes gained) and average reduction family (mean number of genes lost), respectively. (C) The average dN/dS of 5,039 orthologs were determined. Bar charts show the average dN/dS values for six fish species. Data were analyzed using an analysis of variance (ANOVA) followed by Bonferroni post hoc test; values represent mean ± SEM (*P <0.001). (D) In a GO enrichment test among the rapid-evolving genes with dN in the top 10%, 17 GO terms including 46 genes were significantly enriched in N. coriiceps. The average dN/dS of 46 proteins included in enriched GO terms. Bar charts show the average dN/dS values for six fish species. Data were analyzed using an analysis of variance (ANOVA) followed by Bonferroni post hoc tests; values represent mean ± SEM (*P <0.001). (E) The average dN/dS ratio of 20 mitochondrial proteins included in enriched GO terms. Bar charts show the average dN/dS values for six fish species. Data were analyzed using an analysis of variance (ANOVA) followed by Bonferroni post hoc test; values represent mean ± SEM (*P <0.001).