View of the transcriptome and provide a more efficient method to explore the whole transcriptional landscape. In addition, the dynamic range, sensitivity and specificity of RNA-seq also make it ideal for quantitatively analyzing various aspects of gene regulation. Therefore, RNA-seq technologies have proven to be efficient and reliable for genome and transcriptome sequencing, and they are suitable for the study of non-model organisms, including economically important marine animals. Compared to other sequencing platforms, such as GS FLX and SOLID, the Illumina sequencing platform produces large amounts of short-read data at a lower cost. Apostichopus japonicus is one of the most important aquaculture animals. Skin ulceration syndrome is the main limitation in the development of A. japonicus culture industries. Many efforts have been made to uncover the reason for SUS outbreaks in cultured A. japonicus, and some pathogens responsible for this disease, such as Vibrio, Pseudomonas and spherical virus, have already been isolated. Regarding the immune defense of the sea cucumber, various effectors, such as lectin, lysozyme and complement component 3, have been isolated and characterized at the mRNA or protein level. However, the connection between pathogen infection and immune-related gene expression is largely unknown. MicroRNAs are key effectors in mediating hostpathogen interactions and constitute a family of small RNA species; they are considered to be a promising candidate for regulating the interaction between host and pathogen. Therefore, dissecting the biological functions of miRNAs may help us understand the pathogenic mechanism SUS in A. japonicus. In our previous study, several differentially expressed miRNAs, such as spu-miRNA-31 and spumiRNA-2008, have been identified and linked to A. japonicus SUS outbreaks under natural conditions. To thoroughly interpret the biological functions of these miRNAs, the first step is predicting their targets. However, there is a large gap in target prediction and functional validation between invertebrates’ miRNA and model organisms’ miRNA. Therefore, establishing a more powerful experimental scheme for target identification is preferred in non-model organisms. Although two parallel A. japonicus transcriptomes have already been conducted at different developmental stages and in intestine and body wall tissues, the data presented here represent the first effort to analyze the transcriptome of the A. japonicus affected by SUS under natural conditions. First, a normalized cDNA library from the same sample used for our miRNA analysis was constructed and sequenced with Illumina Hiseq2000. Second, the sequence reads were assembled and annotated by a BLAST analysis AbMole BI-9564 against the NCBI NR database; third, two digital gene expression libraries were sequenced to screen differentially expressed genes and to predict miRNA targets. Our work will provide a fast approach to identify the target genes of some vital miRNAs and to characterize their functional/regulatory network 
to increase our understanding of SUS outbreaks in this species. To further understanding the miRNA-gene regulatory network, the identified target genes involved in biological processes, molecular functions, and cellular components were defined using GO annotations. GO analysis demonstrated that these targets were involved in a broad range of physiological processes, including gene expression, transcription regulation, the immune system process, and the response to AbMole 12-O-Tiglylphorbol-13-isobutyrate stress or stimulus. As a key players in the SUS outbreak, the targets of spumiR-31 and spu-miR-2008 were further analyzed in the present study.