Transcriptome analysis reveal alterations in hepatic glycan biosynthesis and metabolism of grass carp (Ctenopharyngodon idellus) fed with broad beans

Abstract

Abstract The meat of grass carp (Ctenopharyngodon idellus) fed broad beans is crispy, called crisp grass carp. In order to better understand the changes mechanistic in liver tissue of crisp grass carp, gene expression profiles and pathways of liver tissues were performed by using RNA-seq. As a result of the transcriptome analysis, the total number of reads produced for each liver sample ranged from 35,914,404 to 42,460,834. A total of 2519 differentially expressed genes (DEGs) were identified. Among them, 1156 genes were up-regulated and 1363 genes were down-regulated. Gene Ontology (GO) annotations indicated that DEGs were mainly enriched in biological processes of ribosome and structural constituent of ribosome. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that DEGs were mainly enriched in metabolism of energy, amino acid, carbohydrate, and lipid acid, and the genes in these pathways were up-regulated. The protein-protein interaction (PPI) network with 260 nodes and 249 edges was constructed and 3 modules were extracted from the entire network. ITML, STT3B, SEL1L, UGGT1, MLEC, IL1B, ALG5, KRTCAP2, NFKB2, IRAK3 genes were the top 10 hub genes with the closest connections to other nodes. In summary, this study identified several candidate genes and focused on glycan biosynthesis and metabolism pathways, providing a reference for further investigation into the mechanism of liver metabolism in grass carp fed with broad beans.