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RNA-seq analysis reveals divergent adaptive response to hyper- and hypo-salinity in cobia, Rachycentron canadum

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Abstract

Salinity is an important abiotic stress that affects metabolic and physiological activities, breed, development, and growth of marine fish. Studies have shown that cobia (Rachycentron canadum), a euryhaline marine teleost fish, possesses the ability of rapid and effective hyper/hypo iono- and osmoregulation. However, genomic studies on this species are lacking and it has not been studied at the transcriptome level to identify the genes responsible for salinity regulation, which affects the understanding of the fundamental mechanism underlying adaptation to fluctuations in salinity. To describe the molecular response of cobia to different salinity levels, we used RNA-seq analysis to identify genes and biological processes involved in response to salinity changes. In the present study, 395,080,114 clean reads were generated and then assembled into 65,318 unigenes with an N50 size of 2758 bp. There were 20,671 significantly differentially expressed genes (DEGs) including 8805 genes adapted to hypo-salinity and 11,866 genes adapted to hyper-salinity. These DEGs were highly represented in steroid biosynthesis, unsaturated fatty acid metabolism, glutathione metabolism, energy metabolism, osmoregulation, and immune response. The candidate genes identified in cobia provide valuable information for studying the molecular mechanism of salinity adaptation in marine fish. Furthermore, the transcriptomic sequencing data acts not only as an important resource for the identification of novel genes but also for further investigations regarding cobia biology.

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Abbreviations

bp:

base pairs (measuring unit)

DEGs:

differential expressed genes

RPKM:

reads per kb per million reads

FDR:

false discovery rate

GO:

gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

NCBI:

National Center for Biotechnology Information

RPKM:

reads per kilobase per million reads

RNA-seq:

RNA-sequencing

Ebp:

emopamil binding protein;

CS:

citrate synthase

IDH:

isocitrate dehydrogenase

LDH:

lactate dehydrogenase

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Acknowledgments

The authors are grateful to the GENE DENOVO Biotechnology Limited Company that offered facilities and technical assistance to run the ion proton sequencer. We also thank the anonymous reviewers for their critical comments.

Availability of data and materials

The RNA sequence data supporting the conclusions of this article are available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA): SRP202920, https://submit.ncbi.nlm.nih.gov/?logout_from=%2Fsubs%2F.

Funding

This work was supported by the China Agriculture Research System (CARS-47). The funding bodies were not involved in the design of the study and collection, analysis, and writing of the manuscript, but provided financial support to cover the costs of the bioassays and sequencing.

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Authors and Affiliations

  1. Department of Aquaculture, College of Fisheries Guangdong Ocean University, Zhanjiang, 524088, Guangdong, People’s Republic of China

    Danyu Cao, Jinfeng Li, Baosong Huang, Jiandong Zhang, Chuanhao Pan, Jiansheng Huang, Hui Zhou, Qian Ma, Gang Chen & Zhongliang Wang

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  1. Danyu Cao
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Contributions

ZW, GC, JZ, CP, JH, HZ, and QM designed the experiments. DC, JL, and BH conducted the experiments. DC and ZW prepared the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Zhongliang Wang.

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The authors declare that there are no conflicts of interest.

Ethics approval and consent to participate

All animal experiments were conducted in accordance with the guidelines and approval of the respective Animal Research and Ethics Committees of Guangdong Ocean University. The field studies did not involve endangered or protected species.

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Additional file 1

S1 Appendix. The primers designed for real-time PCR validation (DOT 32 kb)

Additional file 2

S2 Appendix. List of KEGG pathway analyzed in cobia (XLS 470 kb)

Additional file 3

S3 Appendix. GO terms of differentially expressed genes identified between the 30 ppt and 10 ppt (FigS3-1). GO terms of differentially expressed genes identified between the 30 ppt and 35 ppt (FigS3-2). (DOCX 190 kb)

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Cao, D., Li, J., Huang, B. et al. RNA-seq analysis reveals divergent adaptive response to hyper- and hypo-salinity in cobia, Rachycentron canadum. Fish Physiol Biochem 46, 1713–1727 (2020). https://doi.org/10.1007/s10695-020-00823-7

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