2.10 Gene family identification
The predicted proteomes in the C. undulatus genome and
those from other genomes of 13 teleost fishes, including ballan wrasse
(L. bergylta ), corkwing wrasse (S. melops ), nile tilapia
(Oreochromis niloticus ), clownfish (Amphiprion percula ),
zebrafish (D. rerio ), cave fish (Sinocyclocheilus
anshuiensis ), tongue sole (Cynoglossus semilaevis ), stickleback
(G. aculeatus ), medaka (Oryzias latipes ), mudskipper
(Boleophthalmus pectinirostris ), spotted seabass (L.
maculates ), pufferfish (T. rubripes ), and ghost shark
(Callorhinchus milii ), were filtered to obtain the longest script
per gene, subjected to an all-vs-all Blastp (E-value ≤1e-5), and then
clustered to identify gene family using OrthoMCL (Li et al.2003), with the inflation index set at 1.5 to find orthologs. In the
predicted gene repertoires of the compared genomes, orthologs that could
not be found were ascribed to species-specific genes.