Motif recognition, gene structure, and phylogenetic analysis

The motifs of CRFs were identified with MEME (http://meme-suite.org/tools/meme) [52]. The protein sequences of the identified CRFs were used for multiple-sequence alignment by ClustalW [53] with a gap open penalty of 10 and a gap extension penalty of 0.2, and unrooted phylogenetic trees were generated with the neighbor-joining method with a 1000-replicate bootstrap and other default parameters in MEGA version 6 [54]. The sequence logoes were created by WedLogo 3 (http://weblogo.threeplusone.com/). Finally, the phylogenetic tree of all CRFs was decorated in Itol (http://itol.embl.de/) [55]. The gene structures of CRFs were analyzed and drawn with Gene Structure Display Server (http://gsds.cbi.pku.edu.cn/) [56].