Transcriptome sequencing and metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish (Siniperca chuatsi)

- metabolome analysis of food habits domestication from live prey fish to artificial diets in mandarin fish.
- 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..
- 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.
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- In the wild, as soon as they start to feed, they feed exclusively on live fry of other fish species [1].
- Compared to dead prey fish, the domestication of mandarin fish to accept artificial diets can provide more profitability..
- However, little studies investigate the molecular regu- latory mechanisms of the domestication to accept artificial diets in mandarin fish..
- Previous research showed that the hormones from central nervous systems play important roles in the food intake control, such as neuropeptide Y (NPY) and agouti-related protein (AgRP) [3, 4].
- In giant panda, Tas1r1 pseudogenization reinforced the herbivorous life style because of the diminished attraction of returning to meat eating in the absence of Tas1r1 [5, 6].
- However, little is known about the genetic and metabolic regulation on the food habits domestication of mandarin fish..
- folic acid) to pregnant dams, it was possible to modify the expression of the agouti gene in the off- spring with the high levels of DNA methylation [10, 11].
- The maternal under- nutrition led to a decreased H3K27me3 level of the promotor region and increased expression of pomc gene in offspring mice [12].
- Therefore, whether epi- genetic regulation plays an important role in the food habits domestication is unknown..
- In the present study, we domesticated the mandarin fish to accept artificial diets, and conducted the tran- scriptome sequencing and metabolome analysis to search the common pathways of transcriptome sequen- cing and metabolome.
- In addition, using western blot- ting and bisulfite sequencing PCR, we examined the methylation of histone and DNA, to investigate the mo- lecular mechanism of food habits domestication in man- darin fish, which could promote the culture of mandarin fish with artificial diets..
- Pathway classification map of the differentially expressed genes based on transcriptome sequencing.
- We found 54 genes to be differential expressed among the two groups, 29 and 25 genes are up-regulated and down-regulated in mandarin fish of Group X, respectively.
- The details of the dif- ferential expressed genes between the two groups were presented in Table 1.
- The sequencing data in this study have been deposited in the Sequence Read Archive (SRA) database (accession number: PRJNA613186)..
- We analyzed the metabolic profiles of the two groups by LC-MS in positive (ESI+) and negative (ESI.
- The PCA result showed the positive and negative ions from the dif- ferent groups were in the two clusters, and were separated clearly by the first two components (Fig.
- PLS-DA result showed the clear separation of the two groups (Fig.
- The hierarchical clustering ana- lysis (HCA) of the differential metabolites showed that Group X and W showed significant difference (Fig.
- To identify the metabolites, we used the freely ac- cessible database of Kyoto Encyclopedia of Genes and Genomes (KEGG) to elucidate the putative func- tion of the metabolites.
- In retinol metabolism pathway, retinol, 9-cis-retinol and 11-cis-retinol metabolites were higher in mandarin fish of Group X than those of Group W, RDH (retinol de- hydrogenase) gene expression was consistently higher in Group X (Fig.
- In glycerolipid metabolism pathway, triacylglycerol lipase gene expression was higher in man- darin fish of Group X, and glycerophosphoric metabo- lites was also higher in Group X (Fig.
- In biosynthesis of unsaturated fatty acids pathway, stearoyl- CoA gene expression and DPA (docosapentaenoic acid) metabolites were higher in fish of Group X than those in Group W (Fig.
- TFIIF gene expression and DNA methylation.
- 4a, General transcription factor IIF (TFIIF) gene expression was higher in the mandarin fish of Group X than that of Group W.
- The total DNA methylation level was significantly higher in the fish of Group X than that of Group W (Table 4)..
- Ezh1 gene expression and histone methylation.
- The mRNA expression of histone methyltransferase ezh1 gene was lower in the mandarin fish of Group X (Fig.
- 27’ of histone H3, we analyzed the H3K27me3 levels of the two groups.
- The results showed that H3K27me3 level was also lower in the mandarin fish of Group X than that of Group W (Fig.
- In rearing conditions, mandarin fish accept only live prey fish, refusing dead prey fish or artificial diets [13]..
- Although pervious research showed the methods of mandarin fish domestication [14], little is known about the mechanism of food habits domestication.
- In the present study, we domesticated the mandarin fish to feed on artificial diets, and found a part of mandarin fish could accept artificial diets easily (Group X), but another part could not accept completely (Group W).
- To un- cover the molecular mechanism why mandarin fish re- fuses artificial diets, we conducted the transcriptome sequencing and metabolome analysis.
- The metabolome results showed that the pathways with different metabolites were mostly enriched in the meta- bolic pathways, which were consistent with transcrip- tome sequencing results.
- Previous research has shown that the most important pathways related to the domes- tication of dead prey fish in mandarin fish included the retinal photosensitivity, circadian rhythm, appetite con- trol, learning and memory pathway [2].
- 1 a Pathway classification map of the differentially expressed genes.
- b Rich factor of the differentially expressed genes of different pathway based on transcriptome sequencing.
- showed that metabolism, especially lipid metabolism, might contribute to the domestication of artificial diets, which was different from the domestication of dead prey fish, as the different constituents between dead prey fish and artificial diets..
- For retinol metabolism, retinol, 9-cis-retinol and 11-cis-retinol metabolites were higher in the Group X, consistently the RDH (retinoldehydrogenase) gene ex- pression was higher in the Group X, suggesting a better visual acuity in the mandarin fish which could be easy to.
- accept artificial diets.
- Animals make food choices on the basis of the nutritional, physiological, environmental, and sociocultural factors [7], sensory system is of signifi- cance to food choices.
- It is critical for mandarin fish to catch prey fish though the perception of shape and mo- tion with well-developed scotopic vision [13].
- shows the same motion and shape of food, they have high visual acuity, thus can feed swiftly by darting, the offered food pellet can be captured immediately before it falls down to the bottom of the tank [15–17].
- Because of the low visual acuity and feeding only by stalking, man- darin fish can not recognize the prey before the time when food pellet fall to the bottom of tank, thus makes it difficult to feed mandarin fish with artificial diets [13]..
- The number of all of the differential m/z between the two groups, which including identified ions and unable identified ions MS: the number of identified ions by searching KEGG database associated with primary data (parent ions).
- contributed to the lower visual ability in the mandarin fish which refused artificial diets..
- In glycerolipid metabolism pathway, the gene expres- sion of triacylglycerol lipase was higher in the mandarin fish of Group X, and the glycerophosphoric acid metab- olite was also higher in the Group X.
- In the biosynthesis of unsaturated fatty acids pathway, stearoyl-CoA gene expression and docosapentaenoic acid (DPA) metabolite were higher in the Group X.
- These results suggested that mandarin fish which could accept artificial diets well, might be attributed to the better capacity of glycer- olipid metabolism and unsaturated fatty acids biosyn- thesis.
- Artificial diets might have more fat and energy than live prey fish, suggesting that mandarin fish which accept artificial diets could make good use of fat, while the fish which refuse artificial diets could not..
- To elucidate the regulatory mechanism of up- regulated gene expression in the mandarin fish of Group X, we analyzed the differentially expressed genes based on transcriptome sequencing.
- The results showed TFIIF gene expression was significantly increased in the Group X.
- It suggested that in the man- darin fish which accepted artificial diets, the up- regulated transcription of genes, involved in retinol me- tabolism, glycerolipid metabolism and biosynthesis of unsaturated fatty acids, might be contributed to the in- creased TFIIF expression..
- To uncover why TFIIF was upregulated in the manda- rin fish of Group X, the expressions of histone methyl- transferases were analyzed based on transcriptome.
- The expression of histone-lysine N-methyltransferase ezh1 was significantly decreased in the Group X.
- Furthermore, we observed the protein level of tri- methylation of histone H3 at lysine 27 was lower in the Group X, suggesting an active function of gene expres- sion.
- In addition, the total DNA methylation level of TFIIF was significantly higher in the mandarin fish of Group X than those of Group W.
- The mRNA level of TFIIF was higher in fish of Group X, our results showed a positive effect of DNA methylation on.
- 3 Pathways of the differentially expressed genes and metabolites based on transcriptome and metabolome.
- 4 TFIIF gene expression and DNA methylation.
- a TFIIF gene expression.
- b Illustration of the region of CpG islands sites, which includes 9 CpG sites, DNA methylation patterns of the two groups (X and W) analyzed by BSP.
- Table 4 Methylation of each CpG island of TFIIF gene between the two groups CpG.
- gene expression.
- It is hypothesized that the lower ezh1 expression in the mandarin fish of Group X, could be contributed to the decreased methylation at ‘Lys-27’ of histone H3, and then up-regulating the expression and methylation of TFIIF gene..
- Our research indicated the individual differences of ac- ceptance on artificial diets in mandarin fish and the po- tential molecular mechanism.
- The mandarin fish which feed on artificial diets, could down-regulate the ezh1 ex- pression, repressing the tri-methylation level of histone H3 at lysine 27, and then resulting in the increased DNA methylation and mRNA expression of TFIIF gene..
- TFIIF as an important transcription factor, might regu- late the expression of genes involved in retinol metabol- ism, glycerolipid metabolism and glycerophosphoric metabolism, and modify the acceptance on artificial diets of mandarin fish.
- These results suggested the potential effect of histone methylation on food habits domestica- tion in mandarin fish..
- Mandarin fish g) were obtained from Chin- ese Perch Research Center of Huazhong Agricultural University (Wuhan, Hubei Province, China) and main- tained in the aquarium (12 tanks, 50 fish per tank) at constant temperature C).
- Mandarin fish were.
- and domesticated and fed with artificial diets (Table 5) and divided into two groups: fish did not eat artificial di- ets and fish ate artificial diets.
- The fish did not eat artifi- cial diets during the first domestication process was then fed with live fish prey for three days, starved for two days and fed with artificial diets for one day, and then we selected the fish did not eat artificial diets during the second domestication process and repeated the domesti- cation process for one more time.
- The fish ate artificial diets during the first domestication process was fed with live fish prey for one days and fed with artificial diets for three days, then we selected the fish ate artificial diets during the second domestication process and repeated the domestication process for one more time.
- Finally, the two groups were obtained, the fish did not eat artifi- cial diets or ate artificial diets during all of the three do- mestication processes, named Group W (n = 56) or X (n = 24), respectively.
- Table 5 Composition of artificial diets.
- DNA methylation analysis.
- Six samples from the mandarin fish of Group W or X were analyzed with five technical replicates..
- Table 6 Nucleotide sequences of the primers Primers for real-time PCR Sequences(5 ′ -3.
- mandarin fish through transcriptome analysis.
- Anatomy and regulation of the central melanocortin system.
- Pseudogenization of the umami taste receptor gene Tas1r1 in the giant panda coincided with its dietary switch to bamboo.
- The sequence and de novo assembly of the giant panda genome.
- The role of sense organs in the feeding behaviour of Chinese perch.
- Weaning Chinese perch Siniperca chuatsi (Basilewsky) onto artificial diets based upon its specific sensory modality infeeding.
- Interaction of the human androgen receptor transactivation function with the general transcription factor TFIIF.
- Histone methylation of h3k4 involved in the anorexia of carnivorous mandarin fish (siniperca chuatsi) after feeding on a carbohydrate-rich diet.
- Analysis of relative gene expression data using real- time quantitative PCR and the 2 −ΔΔ CT method.
- DNA methylation of T1R1 gene in the vegetarian adaptation of grass carp ctenopharyngodon idella

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