Differential responses of hepatopancreas transcriptome between fast and slow growth in giant freshwater prawns (Macrobrachium rosenbergii) fed a plant-based diet

Abstract

Efficient utilisation of plant-based diets in the giant freshwater prawn, Marcrobrachium rosenbergii, varies according to individual, suggesting that it might be associated with differences in physiological and metabolic responses. Therefore, we aimed to investigate the individual differences in the growth response of shrimp fed to a soybean-based diet (SBM). Two hundred shrimp were fed SBM for 90 days, and specific growth rate (SGR) was determined individually. Fast- and slow-growing shrimp (F-shrimp vs. S-shrimp), with the highest and lowest 5% SGRs, respectively, were sampled to determine haemolymph chemistry and carcass composition. The hepatopancreas of these shrimps were used for transcriptome analysis through RNA sequencing (RNA-Seq). The results showed no significant differences in haemolymph chemistry parameters. In terms of carcass proximate composition, F-shrimp exhibited higher protein composition than did S-shrimp, suggesting that F-shrimp have higher protein anabolism. Using RNA-seq and real-time reverse transcription polymerase chain reaction (qRT-PCR), the expression levels of several genes encoding physiologic and metabolic enzymes were found to be upregulated in F-shrimp compared to in S-shrimp, suggesting that these enzymes/proteins mediated the efficient use of SBM-based diets for growth promotion in shrimp. Various DEGs associated with the immune system were observed, indicating a difference in immune processes between F- and S-shrimp. The expression of several housekeeping genes was found to be upregulated in S-shrimp. Collectively, the upregulated expression of several enzymes associated with physiological and/or metabolic processes and increased protein anabolism may be attributed to the efficient use of SBM for maximal growth in shrimp.

Keywords: Marcrobrachium rosenbergii; Growth; Hepatopancreas; Plant-based diet; RNA sequencing.

Figure 1

Specific growth rate of experimental fast- and slow- growing shrimps fed an SBM-based diet. Fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp) were selected from the top and bottom 5% SGR, respectively.

Figure 2

Histogram of gene ontology (GO) classification of all genes that were expressed in hepatopancreas of fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp). The results are presented in three main categories: biological process, cellular component, and molecular function.

Figure 3

Classification of all genes annotated in KOG that were expressed in hepatopancreas of fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp). The X-axis represents the classification name of the 26 KOG groups, and the Y-axis represents the percentage of genes in each annotated KOG group.

Figure 4

Classification of all genes annotated in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were expressed in hepatopancreas of fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp). The X-axis represents the percentage of genes in each annotated KEGG pathway, and the Y-axis shows KEGG pathway terms. The KEGG metabolic pathways gene involved in are divided into 5 branches: A: Cellular Processes, B: Environmental Information Processing, C: Genetic Information Processing, D: Metabolism, E: Organismal Systems.

Figure 5

Heatmap plots for differentially expressed transcripts between fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp). Red denotes genes with high expression levels, and green denotes genes with low expression levels. The colours ranging from red to green represent the log10 (FPKM + 1) value from large to small. Only the top 50 DEGs were used to construct the heatmap. The plots were conducted using Plotting tools: R (Version 3.0.3) ggplot2 package, pheatmap package (https://ap-magic.novogene.com/customer/main#/visitor-main/heatmap).

Figure 6

Differential expression of selected genes between fast-growing shrimp (F-shrimp) and slow-growing shrimp (S-shrimp) using qRT-PCR analysis. Selected genes that were crucial in physiologic and metabolic processes including crustapain (cys), crustin (crus), ornithine decarboxylase antizyme-1 (odc-az), 6-phosphogluconate dehydrogenase (6pgd), actin cytoplasmic 1 (actb), tumor necrosis factor alpha-induced protein 8 (tnfaip8), coiled-coil and C2 domain-containing protein 1A (cc2d1a), furry protein (fry), C-type lectin 1 (clec), insulin-like androgenic gland hormone binding protein (iagbp), signal-induced proliferation-associated 1-like protein 2 isoform X2 (sipa1l2), vacuolar protein sorting-associated protein 13A-like isoform X2 (vps13a), Rab GTPase-binding effector protein 1 (rabep1), and friend leukemia integration 1 transcription factor (fli1) have been shown.