Genome-wide investigation of the TGF-β superfamily in scallops
Abstract Background Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09942-w |
| _version_ | 1797363555574480896 |
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| author | Qian Zhang Jianming Chen Wei Wang Jingyu Lin Jiabao Guo |
| author_facet | Qian Zhang Jianming Chen Wei Wang Jingyu Lin Jiabao Guo |
| author_sort | Qian Zhang |
| collection | DOAJ |
| description | Abstract Background Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods. Results Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily. Conclusion Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops. |
| first_indexed | 2024-03-08T16:22:57Z |
| format | Article |
| id | doaj.art-09272b3d66a4418f8ac972c7971bddd3 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T16:22:57Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-09272b3d66a4418f8ac972c7971bddd32024-01-07T12:12:38ZengBMCBMC Genomics1471-21642024-01-0125111310.1186/s12864-023-09942-wGenome-wide investigation of the TGF-β superfamily in scallopsQian Zhang0Jianming Chen1Wei Wang2Jingyu Lin3Jiabao Guo4Institute of Oceanography, College of Geography and Oceanography, Minjiang UniversityInstitute of Oceanography, College of Geography and Oceanography, Minjiang UniversityInstitute of Oceanography, College of Geography and Oceanography, Minjiang UniversityInstitute of Oceanography, College of Geography and Oceanography, Minjiang UniversityInstitute of Oceanography, College of Geography and Oceanography, Minjiang UniversityAbstract Background Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods. Results Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily. Conclusion Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops.https://doi.org/10.1186/s12864-023-09942-wScallopTGF-β superfamilyPhylogenyGene expressionGenome-wide |
| spellingShingle | Qian Zhang Jianming Chen Wei Wang Jingyu Lin Jiabao Guo Genome-wide investigation of the TGF-β superfamily in scallops BMC Genomics Scallop TGF-β superfamily Phylogeny Gene expression Genome-wide |
| title | Genome-wide investigation of the TGF-β superfamily in scallops |
| title_full | Genome-wide investigation of the TGF-β superfamily in scallops |
| title_fullStr | Genome-wide investigation of the TGF-β superfamily in scallops |
| title_full_unstemmed | Genome-wide investigation of the TGF-β superfamily in scallops |
| title_short | Genome-wide investigation of the TGF-β superfamily in scallops |
| title_sort | genome wide investigation of the tgf β superfamily in scallops |
| topic | Scallop TGF-β superfamily Phylogeny Gene expression Genome-wide |
| url | https://doi.org/10.1186/s12864-023-09942-w |
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