The immune response of fairy shrimp Streptocephalus sirindhornae against bacterial black disease by de novo transcriptome analysis.

To enhance genomic resources and to understand the molecular immune mechanisms underlying the response of fairy shrimp (Streptocephalus sirindhornae) to pathogens, we first performed a comparative gene transcription analysis from Aeromonas hydrophila-immunized shrimp and from a control group through RNA sequencing. Meanwhile, the differentially expressed genes (DEGs) were investigated, and a total of 46,958,894 clean reads were obtained and then assembled into 73,297 unigenes with an average length of 993 bp and an N50 of 1,458 bp. Unigenes were annotated by comparison with the NR/NT/KO/SwissProt/PFAM/GO and KOG databases, and 28,198 unigenes (38.47%) were annotated in at least one database. After a bacterial challenge, 143 and 287 genes were identified as markedly up- or downregulated, respectively, and 345 were associated with 142 pathways, including the classic immune-related apoptosis, toll-like receptor and MAPK signaling pathways. Moreover, ten differently expressed immune-related genes were confirmed by using quantitative real-time PCR. This study characterized a gene expression pattern for normal and Aeromonas hydrophila-immunized S. sirindhornae for the first time and shed new light on its molecular mechanisms, thus enabling the future efforts of disease control programs for this valuable aquaculture species.