Genome wide identification of scavenger receptors class A in common carp (Cyprinus carpio) and their expression following Aeromonas hydrophila infection

• Scavenger receptors class A were identified in common carp at whole genome scale.
• SCARA2, SCARA3 and SCARA4 were found have undergone gene duplication.
• The expression patterns were characterized during early developmental stages.
• The expression patterns were examined in various healthy tissues.
• SCARAs were up-regulated in spleen and intestine following bacterial infection.

Scavenger receptors class A (SCARAs) is a subgroup of diverse families of pattern recognition receptors that bind a range of ligands, and play important roles in innate immune processes through pathogens detection, adhesion, endocytosis, and phagocytosis. However, most studies of SCARAs have focused on mammals, and much less is known of SCARAs in fish species. In this study, we identified 7 SCARAs across the common carp genome, which were classified into four subclasses according to comparative genomic analysis including sequence similarities analysis, gene structure and functional domain prediction. Further phylogenetic and syntenic analysis supported their annotation and orthologies. Through examining gene copy number of SCARA genes across several vertebrates, SCARA2, SCARA3 and SCARA4 were found have undergone gene duplication. The expression patterns of SCARAs in common carp were examined during early developmental stages, in healthy tissues, and after Aeromonas hydrophila infection. Most SCARA genes were ubiquitously expressed during common carp early developmental stages, and presented diverse patterns in various healthy tissues, with relatively high expression levels in spleen, liver, intestine, gill and brain, indicating their critical roles likely in maintaining homeostasis and host immune response activities. After A. hydrophila infection, most SCARA genes were up-regulated at 4 h post infection in mucosal tissue intestine, while generally up-regulated at 12 h post infection in spleen, suggesting a tissue-specific pattern of regulation. Taken together, all these results suggested that SCARA genes played important roles in host immune response to A. hydrophila infection in common carp, and provided important genomic resources for future studies on fish disease management.