Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex
Fast-twitch and slow-twitch muscles are the two principal skeletal muscle types in teleost with obvious differences in metabolic and contractile phenotypes. The molecular mechanisms that control and maintain the different muscle types remain unclear yet. Pseudocaranx dentex is a highly mobile active...
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PeerJ Inc.
2022-03-01
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| author | Huan Wang Busu Li Long Yang Chen Jiang Tao Zhang Shufang Liu Zhimeng Zhuang |
| author_facet | Huan Wang Busu Li Long Yang Chen Jiang Tao Zhang Shufang Liu Zhimeng Zhuang |
| author_sort | Huan Wang |
| collection | DOAJ |
| description | Fast-twitch and slow-twitch muscles are the two principal skeletal muscle types in teleost with obvious differences in metabolic and contractile phenotypes. The molecular mechanisms that control and maintain the different muscle types remain unclear yet. Pseudocaranx dentex is a highly mobile active pelagic fish with distinctly differentiated fast-twitch and slow-twitch muscles. Meanwhile, P. dentex has become a potential target species for deep-sea aquaculture because of its considerable economic value. To elucidate the molecular characteristics in the two muscle types of P. dentex, we generated 122 million and 130 million clean reads from fast-twitch and slow-witch muscles using RNA-Seq, respectively. Comparative transcriptome analysis revealed that 2,862 genes were differentially expressed. According to GO and KEGG analysis, the differentially expressed genes (DEGs) were mainly enriched in energy metabolism and skeletal muscle structure related pathways. Difference in the expression levels of specific genes for glycolytic and lipolysis provided molecular evidence for the differences in energy metabolic pathway between fast-twitch and slow-twitch muscles of P. dentex. Numerous genes encoding key enzymes of mitochondrial oxidative phosphorylation pathway were significantly upregulated at the mRNA expression level suggested slow-twitch muscle had a higher oxidative phosphorylation to ensure more energy supply. Meanwhile, expression patterns of the main skeletal muscle developmental genes were characterized, and the expression signatures of Sox8, Myod1, Calpain-3, Myogenin, and five insulin-like growth factors indicated that more myogenic cells of fast-twitch muscle in the differentiating state. The analysis of important skeletal muscle structural genes showed that muscle type-specific expression of myosin, troponin and tropomyosin may lead to the phenotypic structure differentiation. RT-qPCR analysis of twelve DEGs showed a good correlation with the transcriptome data and confirmed the reliability of the results presented in the study. The large-scale transcriptomic data generated in this study provided an overall insight into the thorough gene expression profiles of skeletal muscle in a highly mobile active pelagic fish, which could be valuable for further studies on molecular mechanisms responsible for the diversity and function of skeletal muscle. |
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| spelling | doaj.art-5bc1b410a0ab40b1ad15e6c02575308f2023-12-03T00:46:19ZengPeerJ Inc.PeerJ2167-83592022-03-0110e1272010.7717/peerj.12720Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentexHuan Wang0Busu Li1Long Yang2Chen Jiang3Tao Zhang4Shufang Liu5Zhimeng Zhuang6Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, ChinaYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, ChinaYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, ChinaCollege of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning, ChinaDalian Tianzheng Industry Co., Ltd., Dalian, Liaoning, ChinaYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, ChinaYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, ChinaFast-twitch and slow-twitch muscles are the two principal skeletal muscle types in teleost with obvious differences in metabolic and contractile phenotypes. The molecular mechanisms that control and maintain the different muscle types remain unclear yet. Pseudocaranx dentex is a highly mobile active pelagic fish with distinctly differentiated fast-twitch and slow-twitch muscles. Meanwhile, P. dentex has become a potential target species for deep-sea aquaculture because of its considerable economic value. To elucidate the molecular characteristics in the two muscle types of P. dentex, we generated 122 million and 130 million clean reads from fast-twitch and slow-witch muscles using RNA-Seq, respectively. Comparative transcriptome analysis revealed that 2,862 genes were differentially expressed. According to GO and KEGG analysis, the differentially expressed genes (DEGs) were mainly enriched in energy metabolism and skeletal muscle structure related pathways. Difference in the expression levels of specific genes for glycolytic and lipolysis provided molecular evidence for the differences in energy metabolic pathway between fast-twitch and slow-twitch muscles of P. dentex. Numerous genes encoding key enzymes of mitochondrial oxidative phosphorylation pathway were significantly upregulated at the mRNA expression level suggested slow-twitch muscle had a higher oxidative phosphorylation to ensure more energy supply. Meanwhile, expression patterns of the main skeletal muscle developmental genes were characterized, and the expression signatures of Sox8, Myod1, Calpain-3, Myogenin, and five insulin-like growth factors indicated that more myogenic cells of fast-twitch muscle in the differentiating state. The analysis of important skeletal muscle structural genes showed that muscle type-specific expression of myosin, troponin and tropomyosin may lead to the phenotypic structure differentiation. RT-qPCR analysis of twelve DEGs showed a good correlation with the transcriptome data and confirmed the reliability of the results presented in the study. The large-scale transcriptomic data generated in this study provided an overall insight into the thorough gene expression profiles of skeletal muscle in a highly mobile active pelagic fish, which could be valuable for further studies on molecular mechanisms responsible for the diversity and function of skeletal muscle.https://peerj.com/articles/12720.pdfPseudocaranx dentexFast-twitch muscleSlow-twitch muscleTranscriptome expression profilesDifferentially expressed genes |
| spellingShingle | Huan Wang Busu Li Long Yang Chen Jiang Tao Zhang Shufang Liu Zhimeng Zhuang Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex PeerJ Pseudocaranx dentex Fast-twitch muscle Slow-twitch muscle Transcriptome expression profiles Differentially expressed genes |
| title | Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex |
| title_full | Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex |
| title_fullStr | Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex |
| title_full_unstemmed | Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex |
| title_short | Expression profiles and transcript properties of fast-twitch and slow-twitch muscles in a deep-sea highly migratory fish, Pseudocaranx dentex |
| title_sort | expression profiles and transcript properties of fast twitch and slow twitch muscles in a deep sea highly migratory fish pseudocaranx dentex |
| topic | Pseudocaranx dentex Fast-twitch muscle Slow-twitch muscle Transcriptome expression profiles Differentially expressed genes |
| url | https://peerj.com/articles/12720.pdf |
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