Genome-Wide Identification and Transcriptome-Based Expression Profiling of the Sox Gene Family in the Nile Tilapia (Oreochromis niloticus)

Abstract

The Sox transcription factor family is characterized with the presence of a Sry-related high-mobility group (HMG) box and plays important roles in various biological processes in animals, including sex determination and differentiation, and the development of multiple organs. In this study, 27 Sox genes were identified in the genome of the Nile tilapia (Oreochromis niloticus), and were classified into seven groups. The members of each group of the tilapia Sox genes exhibited a relatively conserved exon-intron structure. Comparative analysis showed that the Sox gene family has undergone an expansion in tilapia and other teleost fishes following their whole genome duplication, and group K only exists in teleosts. Transcriptome-based analysis demonstrated that most of the tilapia Sox genes presented stage-specific and/or sex-dimorphic expressions during gonadal development, and six of the group B Sox genes were specifically expressed in the adult brain. Our results provide a better understanding of gene structure and spatio-temporal expression of the Sox gene family in tilapia, and will be useful for further deciphering the roles of the Sox genes during sex determination and gonadal development in teleosts.

Keywords: Nile tilapia; Sox gene; gene expression; genomic structure; transcriptome.

Figure 1

Exon–intron structure of the tilapia Sox genes. Rectangle and line with double slash indicate exon and intron, respectively. The HMG-box domain regions and the rest regions of the exons are highlighted with green and brown, respectively.

Figure 2

Multiple alignment of HMG-box domain sequences of the tilapia Sox proteins. The HMG-box domain of each Sox protein was predicted online using SMART program (http://smart.embl-heidelberg.de). ClustalX program was used to carry out a multiple alignment of amino acid sequences of the HMG-box domain of all the tilapia Sox proteins.

Figure 3

Phylogenetic tree of the Sox proteins from the tilapia and the other animals. The amino acid sequences of the HMG-box domain of the Sox proteins were used to build a neighbor-joining phylogenetic tree of the Sox genes by using MEGA 6.0 program. The sources of the sequences were described in the Materials and Methods Section. On: Oreochromis niloticus; Ol: Oryzias latipes; Dr: Danio rerio; Fr: Fugu rubripes; Hs: Homo sapiens; Dm: Drosophila melanogaster.

Figure 4

Spatial expression profiles of the tilapia Sox genes. The transcriptomes (NCBI accession number: PRJNA78915 and SRR1916191) of multiple tissues of the adult tilapia were used to profile spatial expression of the tilapia Sox genes. Numbers within the box indicate the RPKM values.

Figure 5

Temporal expression profiles of the Sox genes in the XX and XY gonads of the tilapia. The transcriptomes (NCBI accession number: SRA055700) of the tilapia gonads in four developmental stages comprising of 5, 30, 90 and 180 dah were used to analyze the expression profiles of the Sox genes during gonadal development. Numbers within the box indicate the RPKM values.

Figure 6

Differential expressions of the Sox genes between XX and XY gonads of the tilapia at different developmental stages. The ratio of RPKM value for the expression of each Sox gene in XX (ovary) and XY (testis) gonads in each developmental stage was calculated. If the log2 of the ratio is ≥1 or ≤−1, this Sox gene was considered as sexual dimorphically expressed Sox genes in a developmental stage.

Figure 7

Quantitative RT-PCR examination of the Sox9a (A) and Sox9b (B) expressions in the XX and XY gonads of the tilapia. The quantitative RT-PCR experiment was performed in triplicates using pooled monosex fish cDNAs in each of the selected developmental stages. Values represent the relative mRNA expression in relation to the internal control (β-actin gene). Data were expressed as the mean ± SD of the triplicates. Column error bars with the same letter are not significantly different at p < 0.05 as determined using Least Significant Difference (LSD) test.