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Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress

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Abstract

Fish suffer from starvation due to environmental risks such as extreme weather in the wild and due to insufficient feedings in farms. Nutrient problems from short-term or long-term starvation conditions can result in stress-related health problems for fish. Yellowfin seabream (Acanthopagrus latus) is an important marine economic fish in China. Understanding the molecular responses to starvation stress is vital for propagation and culturing yellowfin seabream. In this study, the transcriptome and genome-wide DNA methylation levels in the livers of yellowfin seabream under 14-days starvation stress were analyzed. One hundred sixty differentially expressed genes (DEGs) by RNA-Seq analysis and 737 differentially methylated-related genes by whole genome bisulfite sequencing analysis were identified. GO and KEGG pathway enrichment analysis found that energy metabolism–related pathways such as glucose metabolism and lipid metabolism were in response to starvation. Using bisulfite sequencing PCR, we confirmed the presence of CpG methylation differences within the regulatory region of a DEG ppargc1a in response to 14-days starvation stress. This study revealed the molecular responses of livers in response to starvation stress at the transcriptomic and whole genome DNA methylation levels in yellowfin seabream.

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Availability of Data and Materials

All the read data were available at the DDBJ database (BioProject Accession:PRJDB13943).

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Acknowledgements

We are grateful to two anonymous reviewers for valuable comments.

Funding

This work was supported by Key-Area Research and Development Program of Guangdong Province (no. 2021B0202020001), Independent Research and Development Projects of Maoming Laboratory (2021ZZ007), and National Natural Science Foundation of China (no. 32072970).

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Authors and Affiliations

  1. College of Life Sciences, State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Yi Long Lin, Zong Xian Zhu, Chun Hui Ai, Ying Ying Xiong, Tong De Liu, Hao Ran Lin & Jun Hong Xia

  2. Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, People’s Republic of China

    Jun Hong Xia

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  1. Yi Long Lin
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Contributions

JHX and HRL contributed to project conception. YLL and CHA collected the materials. YLL, CHA, YYX, ZXZ, and TDL conducted the experiments. Data analysis was conducted by YLL and JHX. The manuscript was prepared by YL and JHX. HRL critically reviewed the manuscript.

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Correspondence to Jun Hong Xia.

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All experiments in this study were approved by the Animal Care and Use Committee of the School of Life Science at Sun Yat-Sen University and were performed according to the regulations and guidelines established by this committee.

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Supplementary Information

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Supplementary Fig 1

GO enrichment of DEGs in liver in response to starvation. DEGs were classified in three GO categories: molecular functions, cellular components and biological processes. The horizontal axis shows each GO term enriched, and the gene number was given after the bar. Blue, green, and red represent molecular functions, cellular components, and biological processes, respectively. (TIF 2403 kb)

Supplementary Fig 2

GO enrichment of DMGs in liver in response to starvation. DMGs were classified in three GO categories: molecular functions, cellular components and biological processes. The horizontal axis shows each GO term enriched, and the gene number was given after the bar. Blue, green, and red represent molecular functions, cellular components, and biological processes, respectively. (TIF 2265 kb)

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Supplementary file7 (DOCX 52 kb)

Supplementary file8 (DOCX 46 kb)

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Lin, Y.L., Zhu, Z.X., Ai, C.H. et al. Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress. Mar Biotechnol 25, 150–160 (2023). https://doi.org/10.1007/s10126-022-10188-y

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