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RNA-seq and microRNA-seq analysis of Japanese flounder (Paralichthys olivaceus) larvae treated by thyroid hormones

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Abstract

Flatfish pigmentation is a complex process, affected by environmental factors including light, nutrients, and hormones. Of those, the thyroid hormone has been reported to increase the albinism rate of Japanese flounder (Paralichthys olivaceus). However, the underlying mechanism remains unclear. In the present study, triiodothyronine (T3), thyroxine, and thiourea were introduced into P. olivaceus larvae from 16 to 57 days after hatching (DAH). By comparison of albinism rate, T3 treatment and control larvae of 42 DAH were chosen for mRNA and miRNA high-throughput sequencing analyses. A total of 337 miRNAs were identified via miRNA-seq, and 12 miRNAs exhibited significantly differential expression patterns in D42_T3 versus D42_Con (TPM > 10, fold change ≥ 1.5 or ≤ 0.67 and q ≤ 0.05). These differentially expressed miRNAs targeted 3658 putative genes, which further enriched to 10 GO terms (q < 0.05). RNA-seq identified 146 differentially expressed genes (DEGs) in D42_T3 versus D42_Con (|log2 fold change| > 1 and q < 0.005), including pigmentation-related genes such as the receptor tyrosine-protein kinase erbB-3, pro-opiomelanocortin A, and melanotransferrin, and the growth-related gene somatotropin. These DEGs were significantly enriched to 15 GO terms and 8 KEGG pathways (q < 0.05), which included several sugar metabolic pathways (glycolysis/gluconeogenesis and the pentose phosphate pathway). Integrated analysis revealed that 26 overlapping genes between DEGs and mRNAs were targeted by miRNAs. Furthermore, seven mRNA-miRNA pairs exhibited reversed regulation patterns. This provides important clues to understand the role of thyroid hormones in flatfish pigmentation.

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Funding

This work was supported by grants from the National Natural Science Foundation of China (31472273, 31461163005), AoShan Talents Cultivation Program Supported by Qingdao National Laboratory for Marine Science and Technology (No.2017ASTCP-OS15), and the Taishan Scholar Climb Project of Shandong Province.

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Authors and Affiliations

  1. Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China

    Na Wang, Renkai Wang, Ruoqing Wang & Songlin Chen

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China

    Na Wang & Songlin Chen

  3. College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China

    Renkai Wang & Ruoqing Wang

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  1. Na Wang
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Correspondence to Na Wang or Songlin Chen.

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Collection and handling of the animals used in this study were approved by Institutional Animal Care and Use Committee (IACUC) of Yellow Sea Fisheries Research Institute, CAFS.

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Wang, N., Wang, R., Wang, R. et al. RNA-seq and microRNA-seq analysis of Japanese flounder (Paralichthys olivaceus) larvae treated by thyroid hormones. Fish Physiol Biochem 45, 1233–1244 (2019). https://doi.org/10.1007/s10695-019-00654-1

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