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

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.

Keywords: Sillago sihama; adaptive evolution; gene expansion; olfactory receptor genes.

Figure 1

Phylogenetic trees of OR genes from S. sihama and six teleost fish functional genomes (n = 745). Phylogenetic trees were constructed using amino acid sequences from seven species (bootstrap copy number: 1000). The phylogenetic tree is divided into six groups (β, γ, δ, ζ, ε, and η). Groups named β to η are signed on the branches. The type I genes are surrounded by the purple line, and the type II genes are surrounded by the pink line.

Figure 2

Conserved motifs of OR genes in S. sihama. Different colors differentiate 10 different motifs. The order of the motifs was 7, 3, 6, 9, 1, 8, 5, 10, 4, and 2. The horizontal axis shows the number of amino acids from the N-terminal to the C-terminal. The OR gene conserved motifs in the red border region belong to type I, while those in the blue border region belong to type II.

Figure 3

Logo representation of the 10 best-conserved motifs in OR genes. The height of the amino acid code represents the conserved degree of the motifs. The height of the letters in the logo indicates the relative frequency of amino acid occurrence, and is proportional to the level of sequence conservation. The sequence outlined by red rectangles was a functionally conserved motif in motifs 1, 2, 3, 4, and 5.

Figure 4

Chromosomal distribution of S. sihama OR genes. The majority of S. sihama OR genes were organized in seven clusters on four chromosomes. The other four OR genes were located on four chromosomes. The genes highlighted in red are expanded genes.

Figure 5

Collinearity relationship of OR genes in S. sihama and L. crocea. Orange bars represent the S. sihama chromosome. Green bars represent the L. crocea chromosome. The grey lines represent the collinearity relationship between S. sihama and L. crocea genes. The red lines represent the collinearity relationship between S. sihama and L. crocea OR genes.

Figure 6

Selection pressure imposed on the OR gene pairs. The X-axis represents the range of the Ka/Ks ratio. The Y-axis represents the number of selection sites detected.

Figure 7

Heatmap of differential expression profile of S. sihama OR genes under different levels of hypoxia related to normal conditions for the gill, heart, and liver. Lighter to darker shades of red and blue indicate increasing upward and decreasing downward regulation of gene expression, respectively. White squares indicate absence of up- or down-regulation.