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

10.21203/rs.3.rs-19835/v1 ◽

2020 ◽

Author(s):

Shan He ◽

Jun-Jie You ◽

Xu-Fang Liang ◽

Zhi-Lu Zhang ◽

Yan-Peng Zhang

Keyword(s):

Dna Methylation ◽

Molecular Mechanism ◽

Food Habits ◽

Artificial Diets ◽

Prey Fish ◽

Mandarin Fish ◽

Metabolome Analysis ◽

Live Prey ◽

Siniperca Chuatsi ◽

Retinol Metabolism

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

10.21203/rs.3.rs-19835/v2 ◽

2020 ◽

Author(s):

Shan He ◽

Jun-Jie You ◽

Xu-Fang Liang ◽

Zhi-Lu Zhang ◽

Yan-Peng Zhang

Keyword(s):

Dna Methylation ◽

Molecular Mechanism ◽

Food Habits ◽

Artificial Diets ◽

Prey Fish ◽

Mandarin Fish ◽

Metabolome Analysis ◽

Live Prey ◽

Siniperca Chuatsi ◽

Retinol Metabolism

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

10.21203/rs.3.rs-19835/v3 ◽

2021 ◽

Author(s):

Shan He ◽

Jun-Jie You ◽

Xu-Fang Liang ◽

Zhi-Lu Zhang ◽

Yan-Peng Zhang

Keyword(s):

Dna Methylation ◽

Molecular Mechanism ◽

Food Habits ◽

Artificial Diets ◽

Prey Fish ◽

Mandarin Fish ◽

Metabolome Analysis ◽

Live Prey ◽

Siniperca Chuatsi ◽

Retinol Metabolism

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Effects of artificial submersed vegetation on consumption and growth of mandarin fish Siniperca chuatsi (Basilewsky) foraging on live prey

Journal of Freshwater Ecology ◽

10.1080/02705060.2018.1561530 ◽

2019 ◽

Vol 34 (1) ◽

pp. 433-444 ◽

Cited By ~ 2

Author(s):

Yan Ren ◽

Mantang Xiong ◽

Jixin Yu ◽

Wei Li ◽

Bo Li ◽

...

Keyword(s):

Mandarin Fish ◽

Live Prey ◽

Siniperca Chuatsi

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A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)

Frontiers in Genetics ◽

10.3389/fgene.2021.671650 ◽

2021 ◽

Vol 12 ◽

Author(s):

Weidong Ding ◽

Xinhui Zhang ◽

Xiaomeng Zhao ◽

Wu Jing ◽

Zheming Cao ◽

...

Keyword(s):

Genome Assembly ◽

Feeding Habit ◽

Mandarin Fish ◽

Fish Genome ◽

Protein Coding ◽

Live Prey ◽

Siniperca Chuatsi ◽

Endocrine Organs ◽

Or Genes ◽

Chromosome Level

The mandarin fish, Siniperca chuatsi, is an economically important perciform species with widespread aquaculture practices in China. Its special feeding habit, acceptance of only live prey fishes, contributes to its delicious meat. However, little is currently known about related genetic mechanisms. Here, we performed whole-genome sequencing and assembled a 758.78 Mb genome assembly of the mandarin fish, with the scaffold and contig N50 values reaching 2.64 Mb and 46.11 Kb, respectively. Approximately 92.8% of the scaffolds were ordered onto 24 chromosomes (Chrs) with the assistance of a previously established genetic linkage map. The chromosome-level genome contained 19,904 protein-coding genes, of which 19,059 (95.75%) genes were functionally annotated. The special feeding behavior of mandarin fish could be attributable to the interaction of a variety of sense organs (such as vision, smell, and endocrine organs). Through comparative genomics analysis, some interesting results were found. For example, olfactory receptor (OR) genes (especially the beta and delta types) underwent a significant expansion, and endocrinology/vision related npy, spexin, and opsin genes presented various functional mutations. These may contribute to the special feeding habit of the mandarin fish by strengthening the olfactory and visual systems. Meanwhile, previously identified sex-related genes and quantitative trait locis (QTLs) were localized on the Chr14 and Chr17, respectively. 155 toxin proteins were predicted from mandarin fish genome. In summary, the high-quality genome assembly of the mandarin fish provides novel insights into the feeding habit of live prey and offers a valuable genetic resource for the quality improvement of this freshwater fish.

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Social Learning of Acquiring Novel Feeding Habit in Mandarin Fish (Siniperca chuatsi)

International Journal of Molecular Sciences ◽

10.3390/ijms20184399 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4399 ◽

Cited By ~ 1

Author(s):

Jian Peng ◽

Ya-Qi Dou ◽

Hui Liang ◽

Shan He ◽

Xu-Fang Liang ◽

...

Keyword(s):

Social Learning ◽

Protein Kinase ◽

Food Intake ◽

Feeding Habits ◽

Feeding Habit ◽

Prey Fish ◽

Mandarin Fish ◽

Live Prey ◽

Learning Group ◽

Dead Prey

Social learning plays important roles in gaining new foraging skills and food preferences. However, the potential role and molecular mechanism of social learning in acquiring new feeding habits is less clear in fish. In the present study, we examined the success rate of feeding habit domestication from live prey fish to dead prey fish, as well as the food intake of dead prey fish in mandarin fish with or without feeders of dead prey fish as demonstrators. Here, we found that mandarin fish can learn from each other how to solve novel foraging tasks, feeding on dead prey fish. In addition, the analysis of gene expressions and signaling pathways of learning through Western blotting and transcriptome sequencing shows that the expression of the c-fos, fra2, zif268, c/ebpd and sytIV genes were significantly increased, and the anorexigenic pomc and leptin a expressions were decreased in fish of the learning group. The phosphorylation levels of protein kinase A (PKA) and Ca2+/calmodulin-dependent protein kinase II (CaMKII) in the learning group were significantly higher than those of the control group, while the phosphorylation level of S6 ribosomal protein (S6) was lower. With the inhibitors of PKA and CaMKII signaling and the chromatin immunoprecipitation (ChIP) assay, we further found that the social learning of new feeding habits in mandarin fish could be attributed to the activation of the CaMKII signaling pathway and then the stimulation of the expression of the c-fos gene, which might be an important transcriptional factor to inhibit the expression of the anorexigenic gene pomc, resulting in the food intake of dead prey fish in mandarin fish. Altogether, our results support the hypothesis that social learning could facilitate the acquisition of novel feeding habits in fish, and it considerably increases the rate of subsequent individual food intake and domestication through the interaction between the learning gene c-fos and the appetite control gene pomc.

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Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding

Communications Biology ◽

10.1038/s42003-020-1094-y ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 2

Author(s):

Shan He ◽

Ling Li ◽

Li-Yuan Lv ◽

Wen-Jing Cai ◽

Ya-Qi Dou ◽

...

Keyword(s):

Feeding Behavior ◽

Model Organisms ◽

Prey Fish ◽

Mandarin Fish ◽

Siniperca Chuatsi ◽

Siniperca Scherzeri ◽

Long Read ◽

Genetic Responses ◽

Genome Assemblies ◽

Gill Raker

AbstractMandarin fishes (Sinipercidae) are piscivores that feed solely on live fry. Unlike higher vertebrates, teleosts exhibit feeding behavior driven mainly by genetic responses, with no modification by learning from parents. Mandarin fishes could serve as excellent model organisms for studying feeding behavior. We report a long-read, chromosomal-scale genome assembly for Siniperca chuatsi and genome assemblies for Siniperca kneri, Siniperca scherzeri and Coreoperca whiteheadi. Positive selection analysis revealed rapid adaptive evolution of genes related to predatory feeding/aggression, growth, pyloric caeca and euryhalinity. Very few gill rakers are observed in mandarin fishes; analogously, we found that zebrafish deficient in edar had a gill raker loss phenotype and a more predatory habit, with reduced intake of zooplankton but increased intake of prey fish. Higher expression of bmp4, which could inhibit edar expression and gill raker development through binding of a Xvent-1 site upstream of edar, may cause predatory feeding in Siniperca.

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