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High throughput, next-generation sequencing techniques have been widely used for gene expression profiling and the study of signal transduction pathways due to their superior advantages over microarray technology, which requires previous genomic sequence or expressed sequence tag information [1]. Whole-transcriptome shotgun sequencing is known as RNA sequencing (RNA-seq) [2], which is a technology that employed the capabilities of next-generation sequencing to reveal a snapshot of the presence and quantity of transcripts in a transcriptome at a given time [3]. RNA-seq can help to capture and annotate the transcriptome [4], and to discover novel transcribed regions in the genomes of non-model aquatic animals [4-6]. It has also been proven to be a sufficient tool to capture the genes and pathways involved in many biological processes of aquatic animals [7-9]. Therefore, the use of RNA-seq has attracted the attention of aquaculture researchers in many areas of research, and successful example studies have been reported in many economical aquaculture species [10-13].
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