Comparative gonad transcriptome analysis in cobia (Rachycentron canadum)

Abstract

Background: Cobia (Rachycentron canadum) is a species of fish with high commercial potential particularly due to fast growth rates. The evidence of sexual size dimorphism favoring females indicate potential benefits in having a monosex culture. However, the involvement of genetic factors responsible for sexual development and gonadal maintenance that produces phenotypic sex in cobia is largely unknown.Methods: In the present study, we performed transcriptome sequencing of cobia to identify sex-biased significantly differentially expressed genes (DEGs) in testes and ovaries. The reliability of the gonad transcriptome data was validated by qPCR analysis of eight selected significantly differential expressed sex-related candidate genes.Results: This comparative gonad transcriptomic analysis revealed that 7,120 and 4,628 DEGs are up-regulated in testes or ovaries, respectively. Further functional annotation analyses identified 76 important candidate genes involved in sex determination cascades or sex differentiation, including 42 known testis-biased DEGs (dmrt1, amh and sox9 etc.), and 34 known ovary-biased DEGs (foxl2, sox3 and cyp19a etc.). Moreover, eleven significantly enriched pathways functionally related to sex determination and sex differentiation were identified, including Wnt signaling pathway, oocyte meiosis, the TGF-beta signaling pathway and MAPK signaling pathway.Conclusion: This work represents the first comparative gonad transcriptome study in cobia. The putative sex-associated DEGs and pathways provide an important molecular basis for further investigation of cobia’s sex determination, gonadal development as well as potential control breeding of monosex female populations for a possible aquaculture setting.

Insights into epigenetic regulation of cyp19a via comparative analysis using the scombrid chub mackerel as model

“…These shared putative TFBSs include Foxl2, Sox3, SF-1, and ESRR, indicating potential roles in gene expression regulation. For instance, Foxl2 has been found to upregulate cyp19a gene expression by directly binding to the promoter in Nile tilapia (Wang et al, 2007), consistent with other studies reporting a female-biased expression of Foxl2 in gonad (Li et al, 2020;Shu et al, 2022;Shen X. et al, 2023). Similarly, we Relative DNA methylation levels in the promoter region of gonad cyp19a for males (blue) and females (pink).…”

“…A sequence spanning approximately 1500bp upstream of the start codon and covering both the first exon and intron, was selected for the analysis. The alignment was conducted with Clustal Omega software (Madeira et al, 2022) and transcription factor binding sites (TFBSs) search was done using JASPAR (Castro-Mondragon et al, 2022) and AnimalTFDB (Shen W et al, 2023) databases. The search was conducted using default parameters, and a minimum relative score of 85% was applied.…”

DataSheet_1.docx

“…These shared putative TFBSs include Foxl2, Sox3, SF-1, and ESRR, indicating potential roles in gene expression regulation. For instance, Foxl2 has been found to upregulate cyp19a gene expression by directly binding to the promoter in Nile tilapia (Wang et al, 2007), consistent with other studies reporting a female-biased expression of Foxl2 in gonad (Li et al, 2020;Shu et al, 2022;Shen X. et al, 2023). Similarly, we Relative DNA methylation levels in the promoter region of gonad cyp19a for males (blue) and females (pink).…”

“…Furthermore, the co-transfection of Foxl2 with SF-1 was shown to have a synergetic influence in the in vitro activation of cyp19a promoter, effect lost when the promoter is hypermethylated (Navarro-Martıń et al, 2011). Likewise, Sox3 has also been found to be differentially higher expressed in females (Li et al, 2020;Shen X. et al, 2023) and is suggested to affect cyp19a transcription by directly binding to the promoter in a frog species (Oshima et al, 2009). The presence of these common regulatory elements across scombrids suggests a conserved regulatory network governing gene expression.…”

“…A sequence spanning approximately 1500bp upstream of the start codon and covering both the first exon and intron, was selected for the analysis. The alignment was conducted with Clustal Omega software (Madeira et al, 2022) and transcription factor binding sites (TFBSs) search was done using JASPAR (Castro-Mondragon et al, 2022) and AnimalTFDB (Shen W et al, 2023) databases. The search was conducted using default parameters, and a minimum relative score of 85% was applied.…”