Fig. 4: Evolution of gene families in the earthworm genome.
a Expansion/constraction of gene families for 12 invertebates. Expanded gene families were shown in green and contracted gene families in red at the whole genome levels. b E. andrei and E. fetida paranome KS distribution and KS distribution of one-to-one orthologs of E. andrei and E. fetida. We constructed and visualized the KS distribution of paralogs and orthologs using ‘ksd’ with default parameters and ‘viz’ command in ‘wgd’ tools, respectively. c Gene families possessing higher proportions of time-dependently DEGs in regeneration. The numbers in the grids were the copy numbers of the gene families for each species. The % column showed the proportion of DEGs in the specific gene family. And the gene families with higher copy numbers were indicated in dark blue, and the gene families with lower copy numbers were indicated in light yellow. For each candidate gene family, a random test was performed by comparing observed numbers of DEGs in regeneration and randomly numbers by using χ2 test. The significant gene families were highlighted with using red p-values. d The epidermal growth factor receptor gene family has a significant expansion in the earthworm compared to other invertebrates. The earthworm has 12 copies (red color), and the other included species only 1–2 copies. Epidermal growth factor receptor (EGFR). And diferent species were showed by using diverse colors. e Transcriptomic analyses of EGFRs during regenerative processes in earthworm. For each regenerative stage of each copy included 5 biological replicates (n = 5). The error bars were showed by using standard error of the mean (s.e.m.). And copies were named by contig’ orders.
