Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi)
Abstract Background As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chuatsi) only feed on live prey fish and refuse artificial diets. In the...
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BMC
2021-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07403-w |
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| author | Shan He Jun-Jie You Xu-Fang Liang Zhi-Lu Zhang Yan-Peng Zhang |
| author_facet | Shan He Jun-Jie You Xu-Fang Liang Zhi-Lu Zhang Yan-Peng Zhang |
| author_sort | Shan He |
| collection | DOAJ |
| description | Abstract Background As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chuatsi) only feed on live prey fish and refuse artificial diets. In the present study, we domesticated mandarin fish to feed on artificial diets. The two groups were obtained, the fish did not eat artificial diets or ate artificial diets during all of the three domestication processes, named Group W or X, respectively. Results Using transcriptome and metabolome analysis, we investigated the differentially expressed genes and metabolites between the two groups, and found three common pathways related to food habit domestication, including retinol metabolism, glycerolipid metabolism, and biosynthesis of unsaturated fatty acids pathways. Furthermore, the western blotting and bisulfite sequencing PCR analysis were performed. The gene expression of TFIIF and histone methyltransferase ezh1 were significantly increased and decreased in the fish of Group X, respectively. The total DNA methylation levels of TFIIF gene and tri-methylation of histone H3 at lysine 27 (H3K27me3) were significantly higher and lower in the fish of Group X, respectively. Conclusion It was speculated that mandarin fish which could feed on artificial diets, might be attributed to the lower expression of ezh1, resulting in the decreased level of H3K27me3 and increased level of DNA methylation of TFIIF gene. The high expression of TFIIF gene might up-regulate the expression of genes in retinol metabolism, glycerolipid metabolism and glycerophosphoric metabolism pathways. Our study indicated the relationship between the methylation of DNA and histone and food habits domestication, which might be a novel molecular mechanism of food habits domestication in animals. |
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| id | doaj.art-7edc50cc5dc845e6b2c526f5087c168e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T09:51:10Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7edc50cc5dc845e6b2c526f5087c168e2022-12-21T23:07:31ZengBMCBMC Genomics1471-21642021-02-0122111210.1186/s12864-021-07403-wTranscriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi)Shan He0Jun-Jie You1Xu-Fang Liang2Zhi-Lu Zhang3Yan-Peng Zhang4College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural UniversityCollege of Fisheries, Chinese Perch Research Center, Huazhong Agricultural UniversityCollege of Fisheries, Chinese Perch Research Center, Huazhong Agricultural UniversityCollege of Fisheries, Chinese Perch Research Center, Huazhong Agricultural UniversityCollege of Fisheries, Chinese Perch Research Center, Huazhong Agricultural UniversityAbstract Background As economical traits, food habits domestication can reduce production cost in aquaculture. However, the molecular mechanism underlying food habits domestication has remained elusive. Mandarin fish (Siniperca chuatsi) only feed on live prey fish and refuse artificial diets. In the present study, we domesticated mandarin fish to feed on artificial diets. The two groups were obtained, the fish did not eat artificial diets or ate artificial diets during all of the three domestication processes, named Group W or X, respectively. Results Using transcriptome and metabolome analysis, we investigated the differentially expressed genes and metabolites between the two groups, and found three common pathways related to food habit domestication, including retinol metabolism, glycerolipid metabolism, and biosynthesis of unsaturated fatty acids pathways. Furthermore, the western blotting and bisulfite sequencing PCR analysis were performed. The gene expression of TFIIF and histone methyltransferase ezh1 were significantly increased and decreased in the fish of Group X, respectively. The total DNA methylation levels of TFIIF gene and tri-methylation of histone H3 at lysine 27 (H3K27me3) were significantly higher and lower in the fish of Group X, respectively. Conclusion It was speculated that mandarin fish which could feed on artificial diets, might be attributed to the lower expression of ezh1, resulting in the decreased level of H3K27me3 and increased level of DNA methylation of TFIIF gene. The high expression of TFIIF gene might up-regulate the expression of genes in retinol metabolism, glycerolipid metabolism and glycerophosphoric metabolism pathways. Our study indicated the relationship between the methylation of DNA and histone and food habits domestication, which might be a novel molecular mechanism of food habits domestication in animals.https://doi.org/10.1186/s12864-021-07403-wMandarin fishTranscriptome sequencingMetabolomeH3K27 tri-methylationDNA methylationFood habits domestication |
| spellingShingle | Shan He Jun-Jie You Xu-Fang Liang Zhi-Lu Zhang Yan-Peng Zhang Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) BMC Genomics Mandarin fish Transcriptome sequencing Metabolome H3K27 tri-methylation DNA methylation Food habits domestication |
| title | Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) |
| title_full | Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) |
| title_fullStr | Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) |
| title_full_unstemmed | Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) |
| title_short | Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi) |
| title_sort | transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish siniperca chuatsi |
| topic | Mandarin fish Transcriptome sequencing Metabolome H3K27 tri-methylation DNA methylation Food habits domestication |
| url | https://doi.org/10.1186/s12864-021-07403-w |
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