2.8 | Expanded and contracted gene families
Based on the phylogenetic tree we constructed using the 2451 single-copy
genes, we explored significant expanded and contracted gene families in
six nematodes (A. suum , B. schroederi , T. canis ,P. univalens , C. elegans and M. hapla ). Gene family
expansion and contraction analyses were performed using CAFÉ (v4.2)(Bie,
Cristianini, Demuth, & Hahn, 2006). We used a median gene number to
estimate the changes in gene family size. The overall P-value of each
gene family were calculated and the details of each branch and node with
the exact P-values of each significant overall P-value (≤ 0.01) gene
family were also calculated. Here we performed analysis in two levels:
1) Comparing gene families of roundworms to other nematode’ to determine
the expanded and contracted genes in roundworms; 2) Comparing theB. schroederi and other three roundworms (A. suum ,P. univalens and T. canis ) to identify gain and loss of
genes in B. schroederi , and then further explain their
differentiation within the roundworm branch.