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. 2017 Aug 14;18(1):613.
doi: 10.1186/s12864-017-3995-9.

Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

Cheng Zhao  1   2 , Guosong Zhang  1   2 , Shaowu Yin  3   4 , Zecheng Li  1   2 , Qintao Wang  1   2 , Shuqiao Chen  5 , Guoqin Zhou  5
Affiliations

Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila)

Cheng Zhao et al. BMC Genomics. .

Abstract

Background: The dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and genetically selective breeding of the dark sleeper. In this study, integrated analysis of mRNA and miRNA was performed on gonad tissue to elucidate the molecular mechanisms of sex determination and differentiation in the dark sleeper.

Results: A total of 143 differentially expressed miRNAs and 16,540 differentially expressed genes were identified. Of these, 8103 mRNAs and 75 miRNAs were upregulated in testes, and 8437 mRNAs and 68 miRNAs were upregulated in ovaries. Integrated analysis of miRNA and mRNA expression profiles predicted more than 50,000 miRNA-mRNA interaction sites, and among them 27,583 negative miRNA-mRNA interactions. A number of sex related genes were targeted by sex-biased miRNAs. The relationship between 15 sex-biased genes and 15 sex-biased miRNAs verified by using qRT-PCR were described. Additionally, a number of SNPs were revealed through the transcriptome data.

Conclusions: The overall results of this study facilitate our understanding of the molecular mechanism underlying sex determination and differentiation and provide valuable genomic information for selective breeding of the dark sleeper.

Keywords: Dark sleeper; Gonads; Sex determination; Sex differentiation; mRNA; miRNA.

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Conflict of interest statement

Ethics approval and consent to participate

All experiments were performed according to the Guidelines for the Care and Use of Laboratory Animals in China. This study was also approved by the Ethics Committee for Experimental Animals at Nanjing Normal University (Permit 91, No. SYXK2015–0028).

Consent for publication

Not applicable.

Competing interests

The authors declare no conflict interests of this article.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Heatmap of the differentially expressed genes of gonads. Heatmap of the count data of gonads for the differentially expressed genes between male and female individuals (Only the top 100 genes are included)
Fig. 2
Fig. 2
Functional annotation of male-biased genes (a) and female-biased genes (b) based on gene ontology (GO) categorization. GO analysis was performed for three main categories: biological process, molecular function, and cellular component
Fig. 3
Fig. 3
KEGG pathways enriched in the male-biased genes (a) and female-biased genes (b)
Fig. 4
Fig. 4
Heatmap of the differentially expressed miRNAs for gonads. Heatmap of the count data of gonads for the differentially expressed miRNAs between male and female individuals (p<0.05)
Fig. 5
Fig. 5
miRNA-mRNA negative correlation network. miRNAs and mRNAs were validated using real-time PCR
See this image and copyright information in PMC

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