DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei).
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| Format: | Artículo científico |
| Langue: | en |
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BMC genomics
2025
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| author | Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng |
| author_facet | Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng |
| collection | PubMed - marine biology |
| contents | DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei). Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng DNA Methylation Animals Penaeidae Metabolic Networks and Pathways Epigenesis, Genetic Promoter Regions, Genetic Gene Expression Profiling DNA methylation is a critical epigenetic modification that dynamically regulates gene expression associated with economic traits. Pacific white shrimp (Litopenaeus vannamei) is one of the most important aquatic species for culturing, and growth trait is one of the most important economic traits for its production. However, research on DNA methylation regulation of growth traits is still at an early stage. This study explored DNA methylome dynamics and their associations with the regulatory mechanism behind growth traits using full-subfamily individuals with discrepant growth performance. The DNA methylation-related genes in L. vannamei were identified, and the expression of DNA methylation genes showed significantly higher levels in the slow growth (SG) group compared to the fast-growing (FG) individuals. The Whole Genome Bisulfite Sequencing (WGBS) analysis revealed that the methylation levels in the muscles of shrimp were notably decreased in SG individuals compared to FG individuals. A total of 532 differentially methylated promoters and 2,067 differentially methylated regions were identified. Through integrative analysis of DNA methylation and transcriptomic data from SG and FG group shrimp, a total of 47 genes were screened out with differential methylation levels (DMGs) and expression levels (DEGs). Functional enrichment analysis revealed that the overlapping DEGs/DMGs were enriched mainly in metabolic pathways, starch and sucrose metabolism, linoleic acid metabolism, ascorbate and aldarate metabolism, pentose and glucuronate interconversions. DNA methylation plays a role in the regulation of growth traits in L. vannamei. The level of DNA methylation was found to be negatively correlated with growth traits. Through comprehensive analysis, it was discovered that DNA methylation predominantly affects growth performance by up-regulating the expression of genes involved in metabolic pathways, such as glucose metabolism and amino acid metabolism in L. vannamei. This suggests a higher metabolism activity in SG individuals derived DNA methylation to cope with some unknown internal stress or environmental stress rather than being allocated for growth. |
| format | Artículo científico |
| id | pubmed_40394505 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | BMC genomics |
| record_format | pubmed |
| spellingShingle | DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei). Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng DNA Methylation Animals Penaeidae Metabolic Networks and Pathways Epigenesis, Genetic Promoter Regions, Genetic Gene Expression Profiling DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei). Zhang, Xin Hu, Chaoqun Chen, Ting Li, Pengying Tan, Yehui Ren, Chunhua Wang, Yanhong Jiang, Xiao Ma, Bo Yin, Jiayue Huang, Yunyi Liu, Liyan Li, Huo Luo, Peng DNA Methylation Animals Penaeidae Metabolic Networks and Pathways Epigenesis, Genetic Promoter Regions, Genetic Gene Expression Profiling DNA methylation is a critical epigenetic modification that dynamically regulates gene expression associated with economic traits. Pacific white shrimp (Litopenaeus vannamei) is one of the most important aquatic species for culturing, and growth trait is one of the most important economic traits for its production. However, research on DNA methylation regulation of growth traits is still at an early stage. This study explored DNA methylome dynamics and their associations with the regulatory mechanism behind growth traits using full-subfamily individuals with discrepant growth performance. The DNA methylation-related genes in L. vannamei were identified, and the expression of DNA methylation genes showed significantly higher levels in the slow growth (SG) group compared to the fast-growing (FG) individuals. The Whole Genome Bisulfite Sequencing (WGBS) analysis revealed that the methylation levels in the muscles of shrimp were notably decreased in SG individuals compared to FG individuals. A total of 532 differentially methylated promoters and 2,067 differentially methylated regions were identified. Through integrative analysis of DNA methylation and transcriptomic data from SG and FG group shrimp, a total of 47 genes were screened out with differential methylation levels (DMGs) and expression levels (DEGs). Functional enrichment analysis revealed that the overlapping DEGs/DMGs were enriched mainly in metabolic pathways, starch and sucrose metabolism, linoleic acid metabolism, ascorbate and aldarate metabolism, pentose and glucuronate interconversions. DNA methylation plays a role in the regulation of growth traits in L. vannamei. The level of DNA methylation was found to be negatively correlated with growth traits. Through comprehensive analysis, it was discovered that DNA methylation predominantly affects growth performance by up-regulating the expression of genes involved in metabolic pathways, such as glucose metabolism and amino acid metabolism in L. vannamei. This suggests a higher metabolism activity in SG individuals derived DNA methylation to cope with some unknown internal stress or environmental stress rather than being allocated for growth. |
| title | DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei). |
| topic | DNA Methylation Animals Penaeidae Metabolic Networks and Pathways Epigenesis, Genetic Promoter Regions, Genetic Gene Expression Profiling |
| url | https://pubmed.ncbi.nlm.nih.gov/40394505/ |