De novo Assembly and Annotation
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters. Then clean data from the samples (skin and brain) were used to do de novo assembly with Trinity (http://trinityrnaseq.sourceforge.net/)(Grabherr et al., 2011). All the assembled transcripts were searched against the NCBI protein nonredundant (NR), String, and KEGG databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set. BLAST2GO (http://www. blast2go.com/ b2ghome)(Conesa et al., 2005) program was used to get GO annotations of unique assembled transcripts for describing biological processes, molecular functions and cellular components. Metabolic pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/)(Goto, 2000).