Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics

Abstract

Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.

Keywords: HMG-box; Japanese quail; SOX; gene family; genomics.

Figure 1

The phylogenetical analyses, categories, and abundance of Sox gene members in galliform birds. Note: The total gene number of T. cupido pinnatus genome is not available in NCBI.

Figure 2

Distribution of the Sox gene family on quail chromosomes.

Figure 3

Phylogenetic tree of the Galliformes Sox family proteins. The tree was constructed using RaxML with the maximum likelihood (ML) method.

Figure 4

Motifs of the quail Sox family genes. Boxes with different numbers represent different motifs. M1 represents the core motif HMG-box (79 amino acids residues and the 3D structure are presented on the right).

Figure 5

Microsynteny related to Sox genes in C. japonica. Triangles represented Sox genes and the flanking genes in the Sox gene family. The gene’s orientation is also represented by the triangle. The homologous genes on two fragments are connected by lines.

Figure 6

Sliding-window plots of representative duplicated Sox gene family members in C. japonica. The step size was 9 bp, and the window size was 150 bp.

Figure 7

Predicted protein–protein interaction (PPI) network analyses of SOX proteins.

Figure 8

Heatmap of expression profiles for the Sox mRNAs in the quails. The color scale represents relative expression levels. The red or green color represented the higher or lower relative abundance of each transcript in each sample. Each column represents one sample, and each row indicates one Sox transcript.

Figure 9

qPCR expression profile of the five quail Sox genes between the incubation period and the post-hatch period in the quail ovaries (A) and testes (B), respectively.