Genome-wide identification and analysis of chemokine receptor superfamily in miiuy croaker, Miichthys miiuy

The chemokine receptor (ChemR) superfamily, which is divided into 4 subfamilies (CXCR, CCR, XCR, and CX3CR), is the main receptors of chemokines in innate immune responses. In the current study, we have identified 27 ChemRs in miiuy croaker: 13 CCR genes, 11 CXCR genes, and 3 XCR genes. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, chromosome locations, evolutionary mechanism, and expression levels upon the bacterial challenge were analyzed. Gene structure and location analysis showed that all ChemR genes contain fewer introns (<= 4) and they are unevenly distributed on the 12 chromosomes. And the XCR subfamily of miiuy croaker don't have the DRY motif of ChemR. Phylogenetic and synteny analysis showed that these genes experienced tandem and segmental duplication event in several species, and tandem duplication might be the main expansion way in miiuy croaker. The major ChemRs of each orthologous group in vertebrates were selected for molecular evolution analysis, the results of which indicated that compared with vertebrates, ChemRs of teleost fishes may have a relatively high evolutionary dynamic. In addition, a total of 21 positively selected codons were detected in vertebrate ChemRs under Model 8. RNA-Seq analysis and qRT-PCR verification demonstrated that CXCR3.2, CXCR5, and XCR1 genes were up-regulated significantly upon the Vibrio harveyi infection. These results provide valuable information for investigating the evolutionary relationships of chemokine receptor superfamily in miiuy croaker and laid the basis for further functional analysis.

Automated summary

In this study, we identified 27 ChemR genes in miiuy croaker and analyzed their characteristics, including gene structure, evolutionary mechanism, and expression levels upon bacterial infection. The results showed that these genes underwent tandem and segmental duplication events during evolution, and teleost fishes' ChemRs may have a higher evolutionary dynamic compared to vertebrates. Additionally, 21 positively selected codons were detected in vertebrate ChemRs under Model 8, and certain genes were significantly up-regulated upon Vibrio harveyi infection, providing valuable information for further functional analysis.