Reconstruction And Analysis Of A Genome-scale Metabolic Network Model For Eyestalk,Y Organ And Hepatopancreas Of Chinese Mitten Crab(Eriocheir Sinensis)

Chinese Mitten Crab(Eriocheir sinensis),known as crab,is an important economic aquatic product in China.The sales of crab increase year by year due to its delicious flavor abundant nutrition and huge market demand.With the large-scale and intensive breeding,some problems appeared in the actual cultivation,such as the low breeding rate of juvenile crab,precocious puberty and decreased ovulation rate Therefore,it is an important issue to investigate the regulation mechanism of growth,development and reproduction of crabWith the rapid development of high-throughput sequencing technology,the research of biological regulation at the molecular level has become the main trend.Using molecular biological methods,a large number of genes and proteins related to the growth have been identified in crabs.After the advent of post-genomics,a large number of omics data is accumulated.How to deal with these data,and How to explore the meaning behind them is becoming the new direction of frontier research.Bioinformatics is such a subject which utilizes these data to explore the secret of life behind the scquencs from the perspective of biological systems and integrity.In this study,we reconstructed the genome-scale metabolic network models of three organs in crabs,the eyestalk,Y organ and hepatopancreas.combined with the network metabolic database by screening and removing the redundant data based on transcriptome sequencing of E.Sinensis.Subsequently.the relationship between the structure and function was analyzed by combining the characteristics of network topology,and the main metabolic pathways and characteristic metabolic pathways of each organ were analyzed.The differential gene expression was also compared with the group injected 5-HT or glucose,or remove of eyestalk.A series of closely related proteins and metabolic pathways were obtained in the growth,molting,nutrient storage and transportation of crabs,which provides a novel way to study the metabolic activities of aquatic organisms from holistic perspective.The main research results are as follow s(1)The eyestalk genome-scale metabolic network model for E.sinensis was reconstructed on the basis of transcriptome sequencing,and then corrected by gap filling,supplementing the transport and exchange reaction,and adding the reaction of non-essential amino acid.The model contains 1304 reactions,1381 unigenes,and 1243 metabolites distributing in 100 pathways.The functional module analysis shows that the eyestalk is the regulating center of the endocrine system of E.sinensis and plays a major role in the regulation of amino acids,carbohydrates and nucleotide metabolism.In the analysis of differential gene expression,there were 135 genes corresponding to the expression of 5-HT and glucose in the experimental group.It was presumed that 5-HT could affect the metabolic activity of the core reaction by changing the differential expression reaction(2)The Y-organ genome-scale metabolic network model contains 1477 reactions,1877 unigenes,and 1408 metabolites,distributed in 100 pathways and a total of 11 subsy stems.Functional modules and degree analysis showed that Y organ had a synthetic pathway of ecdysterone and a metabolic pathway for the synthesis of important amino acids.The differential expression of the unigene of Y-organ after eyestalk ablation showed that 191 unigenes in the network model were up-regulated while 283 down-regulated.All the ecdysteroid sy nthesis related genes were up-regulated.The results were consistent with the fact that the secretion of ecdysone increased after eyestalk ablation(3)Hepatopancreas genome-scale metabolic network model contains 1471 metabolic reactions,1882 genes anda total of 1400 metabolites distributed in 101 pathways.Functional modules analysis indicated that the metabolic pathways in the network model matche the function of lipid metabolism,amino acid metabolism for hepatopancreas.Anaysis of differential expression unigenes between normal and eyestalk ablation group showed that the most significant influence occurred on lipid metabolism which a total of 66 gene expressions have changed.The results were consistent with the fact that the hepatopancreas execute the function of nutrient absorption,storage and utilization in cell.(4)A total of 1182 same reactions were identified by the comparison of the metabolic netw ork models of cycstalks,Y organs and hepatopancreas,indicating that most of the reactions contained in the models were the basic metabolism reactions.Among them,the most important metabolic subsystems are amino acid metabolism,glucose metabolism,lipid metabolism and nucleotide metabolism.In amino acid metabolism,tyrosine metabolism,arginine metabolism,proline metabolism and cystcine metabolism accounted for most of the metabolic reactions.Glycolysis metabolism,phosphoinositol metabolism and TCA cycle metabolic process as the main pathways in glucose metabolism.Reactions in glycerol phosphate metabolism,sphingolipid metabolism and arachidonic acid metabolic take up more than half of the reactions in lipid metabolism.Nucleotides metabolic subsystems are all purine and pyrimidinc metabolic reactions.There were 32 different metabolic pathways and 76 specific reactions in the three network models(22 in eyestalks,36 in Y organ and 18 in hepatopancreas).Important metabolic reactions and pathways related to endocrinology,hormone regulation and nerve conduction were also found including choline,lecithin.5-HT,glutathione and sialic acid metabolic pathways in the models.