During the yolk stage, the nutrients of larvae consumed are from the yolk sac, which greatly affect the survival and quality of fish. The aim of this study was to investigate the metabolic changes, physiological characteristics and the related molecular mechanism of Chinese sturgeon (Acipenser sinensis) larvae during yolk stage by biochemical analyses in combination with transcriptome analysis of larvae at three developmental stages (vertical, flat and benthic). The results showed that both total amino acid and protein contents showed a trend of first decreasing and then increasing. The lipid content was stable in the early stages, but decreased significantly in the benthic stage (P < 0.05). In terms of amino acid profile, the contents of leucine, isoleucine and lysine were relatively high in essential amino acids (EAAs), and the contents of glutamate, aspartate and serine were relatively high in non-essential amino acid (NEAA). As for fatty acid content, the most abundant fatty acids are C16:0 (palmitic acid), C18:1 (oleic acid), C18:2n-6 (linoleic acid) and C22:6n-3 (docosahexaenoic acid, DHA). The results of transcriptome analysis showed that 4936 genes were up-regulated and 3079 genes were down-regulated from vertical stage to flat stage, and 1703 genes were up-regulated and 837 genes were down-regulated from flat stage to benthic stage, respectively. According to KEGG enrichment analysis on the differentially expressed genes (DEGs), the up-regulated DEGs mGlu3, mGlu5, NMDAR, PepT1, TAT1, EAAT3, CYP51A1 and CYP7A1 were significantly enriched in pathways related to the nervous system, protein digestion and absorption, steroid synthesis, cholesterol metabolism and bile acid biosynthesis in early development of larvae. Down-regulated DEGs Drg1, NHP2, KRE33 and MPP10 were enriched in the ribosome biogenetic pathway. In late development, up-regulated DEGs, cGAS, IRF3, TRAF2, MHC-I, MHC-II and TAR2, were enriched in pathways associated with innate and adaptive immunity. Down-regulated DKK2 and FGFRs, ITGAs were enriched in Wnt signaling pathway and PI3K-AKT pathway, respectively. In summary, this study revealed that the larval fish consumed protein as the main nutrient from the vertical stage to the flat stage, while mainly consumed lipid from the flat stage to the benthic stage, and highlighted the pathways of DEGs involved in the nervous system and immune system, which would provide new ideal to the high quality larvae production in Chinese sturgeon, thus benefit species protection.
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