Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)

Abstract

Background Grass carp (Ctenopharyngodon idella) is one of the most widely cultivated fishes in China. High stocking density can reportedly affect fish growth and immunity. Herein we performed PacBio long-read single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to evaluate the effects of high stocking density on grass carp transcriptome. Results SMRT sequencing led to the identification of 33,773 genes (14,946 known and 18,827 new genes). From the structure analysis, 8,009 genes were detected with alternative splicing events, 10,219 genes showed alternative polyadenylation sites and 15,521 long noncoding RNAs. Further, 1,235, 962, and 213 differentially expressed genes (DEGs) were identified in the intestine, muscle, and brain tissues, respectively. We performed functional enrichment analyses of DEGs, and they were identified to be significantly enriched in nutrient metabolism and immune function. The expression levels of several genes encoding apolipoproteins and activities of enzymes involved in carbohydrate enzymolysis were found to be upregulated in the high stocking density group, indicating that lipid metabolism and carbohydrate decomposition were accelerated. Besides, four isoforms of grass carp major histocompatibility complex class II antigen alpha and beta chains in the aforementioned three tissue was showed at least a 4-fold decrease. Conclusions The results suggesting that fish farmed at high stocking densities face issues associated with the metabolism and immune system. To conclude, our results emphasize the importance of maintaining reasonable density in grass carp aquaculture.

Effects of Stocking Density on the Growth Performance, Physiological Parameters, Redox Status and Lipid Metabolism of Micropterus salmoides in Integrated Rice–Fish Farming Systems

“…Under a high stocking density, lipid metabolic enzymes, including fatty acid synthetase, hormone-sensitive triglyceride lipase and lipoprotein lipase, were upregulated in the liver of O. niloticus to adapt to adverse conditions [ 80 ]. Transcriptomic analysis showed that Ctenopharyngodon idella farmed at a high stocking density might face issues associated with abnormal lipid metabolism [ 81 ]. Metabolomic analysis showed that lipid metabolism was repressed by a high stocking density in Brachymystax lenok [ 82 ].…”

Effects of stocking density on the growth performance, mitophagy, endocytosis and metabolism of Cherax quadricarinatus in integrated rice–crayfish farming systems

“…The lipid contents were reduced in liver of gilthead seabream ( Sparus aurata ) and piabanha ( Brycon insignis ) under high stocking density, which may reflect a higher lipid utilization to cope with the stress ( Montero et al, 2001 ; Tolussi et al, 2010 ). Multiple omics analysis showed that high density caused abnormal lipid metabolism in grass carp ( Ctenopharyngodon Idella ) and lenok ( Brachymystax lenok ) ( Liu Y et al, 2019 ; He et al, 2021 ). Similarly, our data exhibited altered lipid metabolism in hepatopancreas of C. quadricarinatus under high stocking density.…”

Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost

“…Immune response in fish is influenced by a variety of circumstances. Exceeding limits of extrinsic stressors such as pathogens, 7 temperature, 8 stocking density, 9 salinity 10 and handling 11 lead to alterations in the fish immune system and also that the pathogens have evolved over the time to escape the immune mechanisms of the host. Therefore, scientists are involved in identifying ways to improve the immune defence of fish due to their importance in global food consumption.…”