Genome-wide identification, evolution, and transcriptome-based expression profiling analysis of suppressors of cytokine signaling (SOCS) in grass carp (Ctenopharyngodon idella)

Abstract

Suppressors of cytokine signaling (SOCS) are a crucial negative regulation family that control a variety of signal transduction pathways in immunity, growth, and development. However, they have not been systematically studied in the important economic fish grass carp (Ctenopharyngodon idella). The accumulation of genomic and transcriptomic resources makes it feasible to conduct a systematic analysis of these genes. In the present study, comprehensive analyses, including genome-wide identification, phylogeny, conserved domain/motif, gene structure, chromosomal location, subcellular localization, gene duplication, and expression patterns of the SOCS gene family in grass carp, were performed, based on genomic and transcriptomic data. Here we identified and characterized 14 SOCS genes (CISH, SOCS1a, SOCS1b, SOCS2, SOCS3a, SOCS3b, SOCS4, SOCS5a, SOCS5b, SOCS6a, SOCS6b, SOCS7, SOCS8, and SOCS9) in grass carp. Phylogenetic analysis of deduced protein sequences suggested that all SOCS members were divided into two main types (Type I and Type II). Multiple sequence alignment and domain analyses showed that some CiSOCS members possess Pfam-SOCS, KIR, and ESS structures, in addition to the typical conserved SOCS-box and SH2 region. Gene structure analysis revealed the presence of 1–3 exons among the majority of SOCS genes. The motifs of CiSOCS proteins in the same subfamily were highly conserved. Most SOCS members are predicted to be located in the nucleus. Insights into gene duplication analysis revealed the important role of segmental duplications for the expansion of SOCS genes in grass carp. Purifying selection seemed to be operated during the evolution and expansion of paralogous SOCS genes. mRNA expression analyses indicated that many members were differentially expressed in multiple tissues after grass carp reovirus or Aeromonas hydrophila infection. Taken together, the present comprehensive and systematic studies of the SOCS family members lay a solid foundation for further functional researches of SOCS genes in grass carp.