Characterization of Spleen Transcriptome of Schizothorax prenanti during Aeromonas hydrophila Infection

Schizothorax prenanti (S. prenanti) is an indigenous fish species and is popularly cultured in southwestern China. In recent years, intensive farming of S. prenanti and water quality deterioration has increased the susceptibility of this fish to various pathogens, including Aeromonas hydrophila (A. hydrophila), which has caused severe damage to S. prenanti production. However, the understanding of molecular immune response of S. prenanti to A. hydrophila infection is still lacking. In order to better comprehend the S. prenanti time series immune response process against A. hydrophila, we conducted the first transcriptomic comparison in S. prenanti spleen at 4, 24, and 48 h after the infection challenge of A. hydrophila against their control counterparts. In total, 628 million clean reads were obtained from 18 libraries and assembled into 262,745 transcripts. After eliminating sequence redundancy, 69,373 unigenes with an average length of 1476 bp were obtained. Comparative analysis revealed 1890 unigenes with significantly differential expression, including 172, 455, 589 upregulated and 27, 676, 551 unigenes downregulated genes for 4, 24, and 48 h post-infection, respectively. Differentially expressed genes (DEGs) were validated using qPCR for 15 randomly selected genes. Enrichment and pathway analysis of DEGs was carried out to understand the functions of the immune-related genes. Our results revealed that many important functional genes relating to complement and coagulation cascades, chemokine signaling pathway, toll-like receptor signaling pathway, NOD-like receptor signaling pathway and leukocyte transendothelial migration were regulated during the infection of A. hydrophila, and the expression of those genes reflected the transcriptome profiles during the challenging stages.