CeRNA profiling and the role in regulating gonadal development in gold pompano
Abstract Background The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long. Consequently, it has prompted researchers to investigate gonadal development process of this fish...
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11220-w |
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| author | Changcan Yang Yijun Zhao Wendong Zhao Hai Huang Quanqi Zhang Jinxiang Liu |
| author_facet | Changcan Yang Yijun Zhao Wendong Zhao Hai Huang Quanqi Zhang Jinxiang Liu |
| author_sort | Changcan Yang |
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| description | Abstract Background The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long. Consequently, it has prompted researchers to investigate gonadal development process of this fish. To gain further insight into the function of competing endogenous RNA (ceRNA) in the gonads of T. ovatus and the regulatory mechanism of the ceRNA network, whole transcriptome libraries were constructed from the testes and ovaries. Results Overall, a total of 96 differentially expressed microRNAs (DE-miRNAs), 2,338 differentially expressed messenger RNAs (DE-mRNAs), 973 differentially expressed long non-coding RNAs (DE-lncRNAs), and 94 differentially expressed circular RNAs (DE-circRNAs) were identified. Additionally, a ceRNA network was constructed, and enrichment analysis confirmed the involvement of numerous pathways in reproduction and gonadal development, including the TGF-β signaling pathway and GnRH signaling pathway. The ceRNA network analysis revealed that the oni-let-7d-1-p3 and PC-3p-112794_13 may play significant roles in T. ovatus gonadal development. And we have observed a possible relationship related to gonadal development involving R-spondin-1 (Rspo1), oni-let-7d-1-p3, and MSTRG.14909.1 (lnc-TGFβR). Dual-luciferase gene reporter system and fluorescence in situ hybridization analyses preliminary verified the regulation relationship between Rspo1 and oni-let-7d-1-p3, as well as lnc-TGFβR and oni-let-7d-1-p3 in the cytoplasm of sertoli cells. Conclusion It is hypothesized that the lnc-TGFβR functions as a sponge for oni-let-7d-1-p3, participating in regulating the process of testis development. These findings could enhance our understanding of ncRNAs in gonadal development. It also provides new insight into the function of ncRNAs and the regulatory relationship of ceRNA between males and females. These results might contribute to discussions on the regulation of ncRNA during gametogenesis. |
| format | Article |
| id | doaj-art-535ed08ca3e643fe8539ce2a3ee8cf54 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-535ed08ca3e643fe8539ce2a3ee8cf542025-01-19T12:11:27ZengBMCBMC Genomics1471-21642025-01-0126111510.1186/s12864-025-11220-wCeRNA profiling and the role in regulating gonadal development in gold pompanoChangcan Yang0Yijun Zhao1Wendong Zhao2Hai Huang3Quanqi Zhang4Jinxiang Liu5MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of ChinaMOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean UniversityMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of ChinaMOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of ChinaAbstract Background The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long. Consequently, it has prompted researchers to investigate gonadal development process of this fish. To gain further insight into the function of competing endogenous RNA (ceRNA) in the gonads of T. ovatus and the regulatory mechanism of the ceRNA network, whole transcriptome libraries were constructed from the testes and ovaries. Results Overall, a total of 96 differentially expressed microRNAs (DE-miRNAs), 2,338 differentially expressed messenger RNAs (DE-mRNAs), 973 differentially expressed long non-coding RNAs (DE-lncRNAs), and 94 differentially expressed circular RNAs (DE-circRNAs) were identified. Additionally, a ceRNA network was constructed, and enrichment analysis confirmed the involvement of numerous pathways in reproduction and gonadal development, including the TGF-β signaling pathway and GnRH signaling pathway. The ceRNA network analysis revealed that the oni-let-7d-1-p3 and PC-3p-112794_13 may play significant roles in T. ovatus gonadal development. And we have observed a possible relationship related to gonadal development involving R-spondin-1 (Rspo1), oni-let-7d-1-p3, and MSTRG.14909.1 (lnc-TGFβR). Dual-luciferase gene reporter system and fluorescence in situ hybridization analyses preliminary verified the regulation relationship between Rspo1 and oni-let-7d-1-p3, as well as lnc-TGFβR and oni-let-7d-1-p3 in the cytoplasm of sertoli cells. Conclusion It is hypothesized that the lnc-TGFβR functions as a sponge for oni-let-7d-1-p3, participating in regulating the process of testis development. These findings could enhance our understanding of ncRNAs in gonadal development. It also provides new insight into the function of ncRNAs and the regulatory relationship of ceRNA between males and females. These results might contribute to discussions on the regulation of ncRNA during gametogenesis.https://doi.org/10.1186/s12864-025-11220-wWhole transcriptomeTrachinotus ovatusCeRNAGonadal development |
| spellingShingle | Changcan Yang Yijun Zhao Wendong Zhao Hai Huang Quanqi Zhang Jinxiang Liu CeRNA profiling and the role in regulating gonadal development in gold pompano BMC Genomics Whole transcriptome Trachinotus ovatus CeRNA Gonadal development |
| title | CeRNA profiling and the role in regulating gonadal development in gold pompano |
| title_full | CeRNA profiling and the role in regulating gonadal development in gold pompano |
| title_fullStr | CeRNA profiling and the role in regulating gonadal development in gold pompano |
| title_full_unstemmed | CeRNA profiling and the role in regulating gonadal development in gold pompano |
| title_short | CeRNA profiling and the role in regulating gonadal development in gold pompano |
| title_sort | cerna profiling and the role in regulating gonadal development in gold pompano |
| topic | Whole transcriptome Trachinotus ovatus CeRNA Gonadal development |
| url | https://doi.org/10.1186/s12864-025-11220-w |
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