Comparison of diploid and triploid Carassius auratus provides insights into adaptation to environmental change
Focusing on adaptation of aquatic organisms, especially fish, can help elucidate complex dynamics in freshwater ecology. The differences in genetic and epigenetic regulation between diploid and triploid Carassius auratus affect survival under eutrophication. To identify the underlying mechanisms that lead to better adaption of triploids than diploids, we compared mRNA and microRNA (miRNA) expressions in liver tissue of diploid and triploid individuals obtained from the Dongting lake water system in central China. Differential expression analysis revealed that 566 transcripts were significantly up-regulated, whereas 758 were down-regulated in triploids; of these differentially expressed transcripts, 33 transcripts including cacna1d, nfkb2, hspa1 and fgfr4 were involved in the MAPK signaling pathway, and eight transcripts were determined to be regulated by seven miRNAs. Additionally, four of 25 differential expressed (DE) transcripts (mhc1, irf7, nfkb2 and pik3c) involving the viral carcinogenesis pathway were regulated by four miRNAs. Furthermore, genetic polymorphisms analysis showed that more heterozygous mutations were detected in triploids than diploids. The dN/dS results revealed that 21 genes were under positive selection (dN/dS>1) in C. auratus complex. We hypothesize that these changes related to genetic and epigenetic regulation may be caused by abiotic stresses, and facilitate adaptation to environmental changes.
Keywordstriploid adapting positive selection differential expression
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This work was supported by the National Natural Science Foundation of China (317023343, 1430088, 31730098), the earmarked fund for China Agriculture Research System (CARS-45), the Key Research and Development Project of Hunan Province (2016NK2128), the Key Research and Development Project of Hunan Province (2016NK2128), Hunan Provincial Natural Science and Technology Major Project (2017NK1031), the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province (20134486), the Construction Project of Key Discipline of Hunan Province and China, Natural Science Foundation of Hunan Province (14JJ2148) and the Scientific Research Fund of Hunan Provincial Education Department (16C0974).
- Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D.S. (2003). microRNA targets in Drosophila. Genome Biol 5, R1.Google Scholar
- Jin, J., Wang, Y., Wu, Z., Hergazy, A., Lan, J., Zhao, L., Liu, X., Chen, N., and Lin, L. (2017). Transcriptomic analysis of liver from grass carp (Ctenopharyngodon idellus) exposed to high environmental ammonia reveals the activation of antioxidant and apoptosis pathways. Fish Shellfish Immunol 63, 444–451.CrossRefPubMedGoogle Scholar
- Liu, X.L., Jiang, F.F., Wang, Z.W., Li, X.Y., Li, Z., Zhang, X.J., Chen, F., Mao, J.F., Zhou, L., and Gui, J.F. (2017). Wider geographic distribution and higher diversity of hexaploids than tetraploids in Carassius species complex reveal recurrent polyploidy effects on adaptive evolution. Sci Rep 7, 5395.CrossRefPubMedPubMedCentralGoogle Scholar
- Marie, V., Gonzalez, P., Baudrimont, M., Boutet, I., Moraga, D., Bourdineaud, J.P., and Boudou, A. (2006). Metallothionein gene expression and protein levels in triploid and diploid oysters Crassostrea gigas after exposure to cadmium and zinc. Environ Toxicol Chem 25, 412.CrossRefPubMedGoogle Scholar
- Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562–578.CrossRefPubMedPubMedCentralGoogle Scholar
- Wang, Y., Jiang, X., Li, Y.F., Wang, S.H., Wang, W.W., and Cheng, G.L. (2014). Spatial and temporal distribution of nitrogen and phosphorus and nutritional characteristics of water in Dongting Lake. Res Environ Sci 27, 484–491.Google Scholar