Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama)

SIMPLE SUMMARY: Silver sillago (Sillago sihama) is highly sensitive to environmental stimuli, which restrict the development of its breeding industry. Olfactory receptor (OR) genes play a critical role in the ecology of stress behavior in fishes. A total of 141 OR genes were identified in S. sihama, including 112 intact genes, 26 truncated genes, and three pseudogenes. The OR genes were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I; and η group belonged to type II. The type I OR genes contained almost all conserved motifs, while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2. OR genes were mostly distributed on LG 1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The OR gene expanded mechanisms revealed that positive selection promotes S. sihama efficient adaptation to environmental changes. ABSTRACT: Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.