Genome-wide identification and analysis of scavenger receptors and their expression profiling in response to Edwardsiella tarda infection in Japanese flounder (Paralichthys olivaceus)

The scavenger receptors (SRs) gene family, as one of pattern recognition receptors, participates in the innate immune response in diverse lineages. However, the systematic identification, characteristics and functions of SRs family are lacking in teleost. Here, we identified all 19 SRs family members in Japanese flounder (Paralichthys olivaceus) based on the genome and transcriptome data. Phylogenetic and Ka/Ks analysis demonstrated that these SRs genes were divided into five classes and all exhibited pronounced purified selection pressures. Whole genome duplication event was found in colec12, scarb2, and lamp1. Gene structure, functional domain and motif distri-bution analyses indicated that SRs within the different subfamilies are severely conservative. SRs genes showed diverse expression patterns in the embryogenesis and unchanged tissues. The regulations of 14 SRs genes in blood, gill and kidney after E. tarda infection suggested their roles in innate immune response. Meanwhile, ten SRs genes were differentially expressed after E. tarda stimulation in macrophages in vitro. Then we proved that PoSCARA3 could suppress the activity of NF-kappa B and AP-1 in HEK 293T cells by dual-luciferase assays. In sum-mary, this study provided valuable basis for further functional characterization and immune functions of SRs genes in P. olivaceus.

Automated summary

This study identified 19 scavenger receptor (SRs) family members in Japanese flounder using genome and transcriptome data. Phylogenetic and Ka/Ks analysis revealed five classes within the SRs genes and evidences of purified selection pressures. The study also found that SRs genes are severely conservative within different subfamilies based on gene structure, functional domain, and motif distribution analyses. Additionally, the study demonstrated the important roles of SRs genes in embryogenesis and innate immune response.