Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala)
Abstract Background Megalobrama amblycephala presents unsynchronized growth, which affects its productivity and profitability. The liver is essential for substance exchange and energy metabolism, significantly influencing the growth of fish. Results To investigate the differential metabolites and ge...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11208-6 |
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| author | Qi Liu Xue Zou Ming Zhao Qianqian Guan Zhaoyang Xuan Lusha Liu Zexia Gao |
| author_facet | Qi Liu Xue Zou Ming Zhao Qianqian Guan Zhaoyang Xuan Lusha Liu Zexia Gao |
| author_sort | Qi Liu |
| collection | DOAJ |
| description | Abstract Background Megalobrama amblycephala presents unsynchronized growth, which affects its productivity and profitability. The liver is essential for substance exchange and energy metabolism, significantly influencing the growth of fish. Results To investigate the differential metabolites and genes governing growth, and understand the mechanism underlying their unsynchronized growth, we conducted comprehensive transcriptomic and metabolomic analyses of liver from fast-growing (FG) and slow-growing (SG) M. amblycephala individuals. A total of 2,097 differentially expressed genes (DEGs) were identified between FG and SG, with 830 genes exhibiting significantly higher expression level in FG. KEGG and GO enrichment analysis indicated that the DEGs with higher expression level were significantly correlated with insulin signaling pathway, steroid hormone and lipid metabolism related pathway (PPAR signaling pathway and fatty acid degradation). In the metabolomic analysis, 224 differentially expressed metabolites (DEMs) were detected, of which 128 were significantly more abundant in FG. These more abundant DEMs were prominently enriched in pathways associated with cell proliferation and energy metabolism (Oxidative phosphorylation, mTOR signaling pathway and FoxO signaling pathway). In addition, DEGs and DEMs in adenosine diphosphate (ATP) hydrolysis activity and associate with fatty acid metabolism, glucose metabolism, and amino acid metabolism pathways were both found in the transcriptomic and metabolomic integrated data. These findings suggest that the large amounts of energy generated by fatty acid, glucose metabolism and other energy metabolism pathway promote the rapid growth of FG. Conclusions This research is the first to integrate metabolomic and transcriptomic analyses of liver to identify key genes, metabolites, and pathways to uncover the molecular and metabolic mechanisms of unsynchronized growth in M. amblycephala. The identified metabolic and genes can be potential targets for selective breeding programs to improve growth performance in aquaculture. |
| format | Article |
| id | doaj-art-e624986a9cfa48ea8402192cd55d3220 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-e624986a9cfa48ea8402192cd55d32202025-01-19T12:11:25ZengBMCBMC Genomics1471-21642025-01-0126111210.1186/s12864-025-11208-6Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala)Qi Liu0Xue Zou1Ming Zhao2Qianqian Guan3Zhaoyang Xuan4Lusha Liu5Zexia Gao6College of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityCollege of Fisheries, Huazhong Agricultural UniversityAbstract Background Megalobrama amblycephala presents unsynchronized growth, which affects its productivity and profitability. The liver is essential for substance exchange and energy metabolism, significantly influencing the growth of fish. Results To investigate the differential metabolites and genes governing growth, and understand the mechanism underlying their unsynchronized growth, we conducted comprehensive transcriptomic and metabolomic analyses of liver from fast-growing (FG) and slow-growing (SG) M. amblycephala individuals. A total of 2,097 differentially expressed genes (DEGs) were identified between FG and SG, with 830 genes exhibiting significantly higher expression level in FG. KEGG and GO enrichment analysis indicated that the DEGs with higher expression level were significantly correlated with insulin signaling pathway, steroid hormone and lipid metabolism related pathway (PPAR signaling pathway and fatty acid degradation). In the metabolomic analysis, 224 differentially expressed metabolites (DEMs) were detected, of which 128 were significantly more abundant in FG. These more abundant DEMs were prominently enriched in pathways associated with cell proliferation and energy metabolism (Oxidative phosphorylation, mTOR signaling pathway and FoxO signaling pathway). In addition, DEGs and DEMs in adenosine diphosphate (ATP) hydrolysis activity and associate with fatty acid metabolism, glucose metabolism, and amino acid metabolism pathways were both found in the transcriptomic and metabolomic integrated data. These findings suggest that the large amounts of energy generated by fatty acid, glucose metabolism and other energy metabolism pathway promote the rapid growth of FG. Conclusions This research is the first to integrate metabolomic and transcriptomic analyses of liver to identify key genes, metabolites, and pathways to uncover the molecular and metabolic mechanisms of unsynchronized growth in M. amblycephala. The identified metabolic and genes can be potential targets for selective breeding programs to improve growth performance in aquaculture.https://doi.org/10.1186/s12864-025-11208-6TranscriptomeMetabolomeLiverGrowth differenceMegalobrama amblycephala |
| spellingShingle | Qi Liu Xue Zou Ming Zhao Qianqian Guan Zhaoyang Xuan Lusha Liu Zexia Gao Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) BMC Genomics Transcriptome Metabolome Liver Growth difference Megalobrama amblycephala |
| title | Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) |
| title_full | Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) |
| title_fullStr | Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) |
| title_full_unstemmed | Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) |
| title_short | Integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt-snout bream (Megalobrama amblycephala) |
| title_sort | integrated transcriptome and metabolome analysis of liver reveals unsynchronized growth mechanisms in blunt snout bream megalobrama amblycephala |
| topic | Transcriptome Metabolome Liver Growth difference Megalobrama amblycephala |
| url | https://doi.org/10.1186/s12864-025-11208-6 |
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