Gene family dynamics in the genome
Significant expansion and contraction of gene families may denote environmental adaptation of the species. Based on both divergence time estimation and OrthoMCL gene family clustering, CAFE was used to detect dynamics of gene families residing in the genome. The analysis detected 431 expanded gene families, as well as 491 contracted gene families, in the T. dalaica genome. The top three enriched pathways for expanded family genes were “Gap junction”, “Relaxin signaling pathway”, and “Bile secretion”, while for contracted family genes, the top three were “Estrogen signaling pathway”, “Dopaminergic synapse”, and “Parathyroid hormone synthesis, secretion, and action” (Table S6).