Transcriptome is a total set of transcripts, mRNA, and noncoding RNA, in one or a population of cells during a specific developmental stage or in response to a particular physiological condition using high-throughput technology . It is the connection between genome genetic information and proteomics biological function . In nonstandard model organisms where genomic resources are lacking, such as a fully sequenced genome, obtaining a transcriptome is an effective way to evaluate gene expression and perform comparative studies at the whole genome level . Comparative transcriptome analysis provides the foundation for gene structure and function research and determines when genes are expressed and how they are regulated . Now, it is being widely applied to elucidate genetic factors conferring economically significant traits in cultured crustacean species [26–28].