Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>)
In aquaculture, the Chinese soft-shelled turtle (<i>Pelodiscus sinensis</i>) is an economically important species with remarkable gender dimorphism in its growth patterns. However, the underlying molecular mechanisms of this phenomenon have not been elucidated well. Here, we conducted a...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-05-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/11/6/834 |
| _version_ | 1797489896858845184 |
|---|---|
| author | Junxian Zhu Luo Lei Chen Chen Yakun Wang Xiaoli Liu Lulu Geng Ruiyang Li Haigang Chen Xiaoyou Hong Lingyun Yu Chengqing Wei Wei Li Xinping Zhu |
| author_facet | Junxian Zhu Luo Lei Chen Chen Yakun Wang Xiaoli Liu Lulu Geng Ruiyang Li Haigang Chen Xiaoyou Hong Lingyun Yu Chengqing Wei Wei Li Xinping Zhu |
| author_sort | Junxian Zhu |
| collection | DOAJ |
| description | In aquaculture, the Chinese soft-shelled turtle (<i>Pelodiscus sinensis</i>) is an economically important species with remarkable gender dimorphism in its growth patterns. However, the underlying molecular mechanisms of this phenomenon have not been elucidated well. Here, we conducted a whole-transcriptome analysis of the female and male gonads of <i>P. sinensis</i>. Overall, 7833 DE mRNAs, 619 DE lncRNAs, 231 DE circRNAs, and 520 DE miRNAs were identified. Some “star genes” associated with sex differentiation containing <i>dmrt1</i>, <i>sox9</i>, and <i>foxl2</i> were identified. Additionally, some potential genes linked to sex differentiation, such as <i>bmp2</i>, <i>ran</i>, and <i>sox3</i>, were also isolated in <i>P. sinensis</i>. Functional analysis showed that the DE miRNAs and DE ncRNAs were enriched in the pathways related to sex differentiation, including ovarian steroidogenesis, the hippo signaling pathway, and the calcium signaling pathway. Remarkably, a lncRNA/circRNA–miRNA–mRNA interaction network was constructed, containing the key genes associated with sex differentiation, including <i>fgf9</i>, <i>foxl3</i>, and <i>dmrta2</i>. Collectively, we constructed a gender dimorphism profile of the female and male gonads of <i>P. sinensis</i>, profoundly contributing to the exploration of the major genes and potential ncRNAs involved in the sex differentiation of <i>P. sinensis</i>. More importantly, we highlighted the potential functions of ncRNAs for gene regulation during sex differentiation in <i>P. sinensis</i> as well as in other turtles. |
| first_indexed | 2024-03-10T00:23:11Z |
| format | Article |
| id | doaj.art-d4fad3429ccb463ca194edae7afc9b8b |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T00:23:11Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-d4fad3429ccb463ca194edae7afc9b8b2023-11-23T15:39:02ZengMDPI AGBiology2079-77372022-05-0111683410.3390/biology11060834Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>)Junxian Zhu0Luo Lei1Chen Chen2Yakun Wang3Xiaoli Liu4Lulu Geng5Ruiyang Li6Haigang Chen7Xiaoyou Hong8Lingyun Yu9Chengqing Wei10Wei Li11Xinping Zhu12Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaKey Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, ChinaIn aquaculture, the Chinese soft-shelled turtle (<i>Pelodiscus sinensis</i>) is an economically important species with remarkable gender dimorphism in its growth patterns. However, the underlying molecular mechanisms of this phenomenon have not been elucidated well. Here, we conducted a whole-transcriptome analysis of the female and male gonads of <i>P. sinensis</i>. Overall, 7833 DE mRNAs, 619 DE lncRNAs, 231 DE circRNAs, and 520 DE miRNAs were identified. Some “star genes” associated with sex differentiation containing <i>dmrt1</i>, <i>sox9</i>, and <i>foxl2</i> were identified. Additionally, some potential genes linked to sex differentiation, such as <i>bmp2</i>, <i>ran</i>, and <i>sox3</i>, were also isolated in <i>P. sinensis</i>. Functional analysis showed that the DE miRNAs and DE ncRNAs were enriched in the pathways related to sex differentiation, including ovarian steroidogenesis, the hippo signaling pathway, and the calcium signaling pathway. Remarkably, a lncRNA/circRNA–miRNA–mRNA interaction network was constructed, containing the key genes associated with sex differentiation, including <i>fgf9</i>, <i>foxl3</i>, and <i>dmrta2</i>. Collectively, we constructed a gender dimorphism profile of the female and male gonads of <i>P. sinensis</i>, profoundly contributing to the exploration of the major genes and potential ncRNAs involved in the sex differentiation of <i>P. sinensis</i>. More importantly, we highlighted the potential functions of ncRNAs for gene regulation during sex differentiation in <i>P. sinensis</i> as well as in other turtles.https://www.mdpi.com/2079-7737/11/6/834<i>Pelodiscus sinensis</i>whole-transcriptome sequencingsex differentiationnon-coding RNAsceRNA |
| spellingShingle | Junxian Zhu Luo Lei Chen Chen Yakun Wang Xiaoli Liu Lulu Geng Ruiyang Li Haigang Chen Xiaoyou Hong Lingyun Yu Chengqing Wei Wei Li Xinping Zhu Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) Biology <i>Pelodiscus sinensis</i> whole-transcriptome sequencing sex differentiation non-coding RNAs ceRNA |
| title | Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) |
| title_full | Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) |
| title_fullStr | Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) |
| title_full_unstemmed | Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) |
| title_short | Whole-Transcriptome Analysis Identifies Gender Dimorphic Expressions of Mrnas and Non-Coding Rnas in Chinese Soft-Shell Turtle (<i>Pelodiscus sinensis</i>) |
| title_sort | whole transcriptome analysis identifies gender dimorphic expressions of mrnas and non coding rnas in chinese soft shell turtle i pelodiscus sinensis i |
| topic | <i>Pelodiscus sinensis</i> whole-transcriptome sequencing sex differentiation non-coding RNAs ceRNA |
| url | https://www.mdpi.com/2079-7737/11/6/834 |
| work_keys_str_mv | AT junxianzhu wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT luolei wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT chenchen wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT yakunwang wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT xiaoliliu wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT lulugeng wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT ruiyangli wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT haigangchen wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT xiaoyouhong wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT lingyunyu wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT chengqingwei wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT weili wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi AT xinpingzhu wholetranscriptomeanalysisidentifiesgenderdimorphicexpressionsofmrnasandnoncodingrnasinchinesesoftshellturtleipelodiscussinensisi |