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Science China Life Sciences

, Volume 61, Issue 11, pp 1407–1419 | Cite as

Comparison of diploid and triploid Carassius auratus provides insights into adaptation to environmental change

  • Li Ren
  • Xin Gao
  • Conghui Yang
  • Hui Tan
  • Jialin Cui
  • Shi Wang
  • Wuhui Li
  • Chun Zhang
  • Min Tao
  • Qinbo Qin
  • Shaojun LiuEmail author
Research Paper

Abstract

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.

Keywords

triploid adapting positive selection differential expression 

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Notes

Acknowledgements

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).

Supplementary material

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Supplementary Table 3.The information of differential expression genes in MAPK signaling pathway.
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Supplementary Table 4.The information of differential expression genes in viral carcinogenesis pathway.
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Supplementary table 9. The gain of heterozygous loci distributed in 1783 transcripts in triploid
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Supplementary Table 10. The mergeing of heterozygous loci (⩾ 3) in triploid as compared with diploid
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Supplentary Table 12. The different number of InDel (⩾10) between diploid and triploid
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11427_2017_9358_MOESM11_ESM.jpg (203 kb)
Supplementary material, approximately 641 KB.

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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Li Ren
    • 1
    • 2
  • Xin Gao
    • 1
    • 2
  • Conghui Yang
    • 1
    • 2
  • Hui Tan
    • 1
    • 2
  • Jialin Cui
    • 1
    • 2
  • Shi Wang
    • 1
    • 2
  • Wuhui Li
    • 1
    • 2
  • Chun Zhang
    • 1
    • 2
  • Min Tao
    • 1
    • 2
  • Qinbo Qin
    • 1
    • 2
  • Shaojun Liu
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory of Developmental Biology of Freshwater FishHunan Normal UniversityChangshaChina
  2. 2.College of Life SciencesHunan Normal UniversityChangshaChina

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