Transcriptomic analysis provides insight into the mechanism of salinity adjustment in swimming crab Portunus trituberculatus

  • Baoquan Gao
  • Dongfang Sun
  • Jianjian Lv
  • Xianyun Ren
  • Ping LiuEmail author
  • Jian Li
Research Article



Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the swimming crab (Portunus trituberculatus) is adaptive to relatively low salinity. However, the mechanisms underlying salinity stress responses in P. trituberculatus is not very clear.


The primary objective of this study was to describe the salinity adaptation mechanism in P. trituberculatus.


The crabs were exposed to low salinity stress, and gill tissue was sampled at 0, 12, 36, 48 and 72 h and subjected to high throughput sequencing. Subsequently, we tested the accuracy and quality of the sequencing results, and then carried out GO and KEGG bioinformatics on the differentially expressed genes (DEG).


Each sample yielded more than 1.1 Gb of clean data and 23 million clean reads. The process was divided into early (0–12 h), middle (12–48 h), and late phase (48–72 h). A total of 1971 (1373 up-regulated, 598 down-regulated), 1212 (364 up-regulated, 848 down-regulated), and 555 (187 up-regulated, 368 down-regulated) DEGs with annotations were identified during the three stages, respectively. DEGs were mainly associated with lipid metabolism energy metabolism, and signal transduction from the three stages, respectively.


A substantial number of genes were modified by salinity stress, along with a few important salinity acclimation pathways. This work provides valuable information on the salinity adaptation mechanism in P. trituberculatus. In addition, the comprehensive transcript sequences reported in this study provide a rich resource for identification of novel genes in this and other crab species.


Transcriptomics Salinity adjustment Swimming crab Portunus trituberculatus 



This research was supported by the National Natural Science Foundation of China (Grant nos. 41506186, 41876187 and 41576147), and the Key Research and Development Plan of Shandong Province (2016GSF115028), Jiangsu Science and Technology Department (BE2017325).

Compliance with ethical standards

Conflict of interest

Baoquan Gao, Dongfang Sun, Jianjian Lv, Xianyun Ren, Ping Liu, Jian Li declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors. The study protocol was approved by the Experimental Animal Ethics Committee, Yellow Sea Research Institute, Chinese Academy of Fishery Sciences, China.

Supplementary material

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  1. Abdi H (2007) Bonferroni and Sidak corrections for multiple comparisons. Encyclopedia of measurement and statistics. Sage, Thousand Oaks, pp 103–107Google Scholar
  2. Ana C, Stefan GT, Juan MGG, Javier T, Manuel T, Montserrat R (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefGoogle Scholar
  3. Andre P (1995) Osmotic regulation in crustaceans. J Crustac Biol 15:1–60CrossRefGoogle Scholar
  4. Audic S, ClaverieL JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995CrossRefGoogle Scholar
  5. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188CrossRefGoogle Scholar
  6. Benoit MA, Debauche Devos P (1994) Phosphofructokinase from the posterior gills of the euryhaline crab, Eriocheir sinensis: evidence for its regulation by phosphorylation. J Comp Physiol B 164:165–171CrossRefGoogle Scholar
  7. Brichon G, Babili ME, Zwingelstein G (1996) Does sphingomyelin participate in signal transduction in gill cells of euryhalin crabs during salinity changes? Comp Biochem Physiol B Comp Biochem 115:7–12CrossRefGoogle Scholar
  8. Chapelle S, Dandrifosse G, Zwingelstein G (1976) Metabolism of phospholipids of anterior or posterior gills of the crab Eriocheir sinensis M. EDW, during the adaptation of this animal to media of various salinities. Int J Biochem 7:343–351CrossRefGoogle Scholar
  9. Danulat E (2010) The effects of various diets on chitinase and β-glucosidase activities and the condition of cod, Gadus morhua (L.). J Fish Biol 28:191–197CrossRefGoogle Scholar
  10. Engel DW, Ferguson RL, Eggert LD (1975) Respiration rates and ATP concentrations in the excised gills of the blue crab as a function of salinity. Comp Biochem Physiol A Comp Physiol 52:669–673CrossRefGoogle Scholar
  11. Finn RD, John T, Jaina M (2008) The Pfam protein families database. Nucleic Acids Res 36:281–288CrossRefGoogle Scholar
  12. Fishery Bureau, Ministry of Agriculture, China (2018) China fisheries yearbook. Chinese Agriculture Express, Beijing, p 27Google Scholar
  13. Freire C, Onken H, Mcnamara J (2008) A structure–function analysis of ion transport in crustacean gills and excretory organs. Comp Biochem Physiol A Mol Integr Physiol 151:272–304CrossRefGoogle Scholar
  14. Han XL, Ping L, Gao BQ, Wang HF, Duan YF, Xu WF, Chen P (2015) Na+/K+-ATPase α-subunit in swimming crab Portunus trituberculatus: molecular cloning, characterization, and expression under low salinity stress. Chin J Oceanol Limnol 33:828–837CrossRefGoogle Scholar
  15. Huni AAD, Aravindan CM (1985) The effect of salinity on the oxygen consumption of two intertidal crustaceans. Comp Biochem Physiol Part A Physiol 81:869–871CrossRefGoogle Scholar
  16. Jiang S, Xu HQ (2011) Influence of salinity stress on the activity of gill Na+/K+-ATPase in swimming crab (Portunus trituberculatus). J Fish China 35:1475–1480Google Scholar
  17. Kim YK, Watanabe S, Kaneko T, Huh MD, Park S (2010) Expression of aquaporins 3, 8 and 10 in the intestines of freshwater- and seawater-acclimated Japanese eels Anguilla japonica. Fish Sci 76:695–702CrossRefGoogle Scholar
  18. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360CrossRefGoogle Scholar
  19. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:25CrossRefGoogle Scholar
  20. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform 12:323CrossRefGoogle Scholar
  21. Li XG, Xu ZQ ZQ, Zhou G, Lin H, Zhou J, Zeng QF, Mao ZG, Gu XH (2015) Molecular characterization and expression analysis of five chitinases associated with molting in the Chinese mitten crab, Eriocheir sinensis. Comp Biochem Physiol B: Biochem Mol Biol 187:110–120CrossRefGoogle Scholar
  22. Li L, Pan LQ, Hu DX, Liu D, Liu MQ (2017) The effect of bilateral eyestalk ablation on signal transduction pathways of ion regulation of Litopenaeus vannamei. J World Aquac Soc 48:145–155CrossRefGoogle Scholar
  23. Liu Y, Liu RL, Ye LC, Liang J, Xuan FJ, Xu QH (2009) Genetic differentiation between populations of swimming crab Portunus trituberculatus along the coastal waters of the East China Sea. Hydrobiologia 618:125–137CrossRefGoogle Scholar
  24. Lu YL, Wang F, Zhao ZY, Dong SL, Ma S (2012) Effects of salinity on growth, molt and energy utilization of juvenile swimming crab Portunus trituberculatus. J Fish Sci China 19:237–245Google Scholar
  25. Lv JJ, Liu P, Wang Y, Gao BQ, Chen P, Li J (2013) Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS One 8:e82155CrossRefGoogle Scholar
  26. Lv JJ, Zhang DN, Liu P, Jian Li (2016) Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait. Cell Stress Chaperones 5:1–8Google Scholar
  27. Mcnamara JC, Faria SC (2012) Evolution of osmoregulatory patterns and gill ion transport mechanisms in the decapod Crustacea: a review. J Comp Physiol B 182:997–1014CrossRefGoogle Scholar
  28. Mo JL, Devos P, Trausch G (2003) Active absorption of Cl and Na+ in posterior gills of chinese crab Eriocheir sinensis: modulation by dopamine and cAMP. J Crustac Biol 23:505–512CrossRefGoogle Scholar
  29. Morgan JD, Iwama GK (1991) Effects of salinity on growth, metabolism, and ion regulation in juven. Journal Canadien Des Sciences Halieutiques Et Aquatiques 48:2083–2094CrossRefGoogle Scholar
  30. Morris RJ, Lockwood APM, Dawson ME (1982) An effect of acclimation salinity on the fatty acid composition of the gill phospholipids and water flux of the amphipod crustacean Gammarus duebeni. Comp Biochem Physiol A Physiol 72:497–503CrossRefGoogle Scholar
  31. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Method 5:621–628CrossRefGoogle Scholar
  32. Porter RK, Hulbert AJ, Brand MD (1996) Allometry of mitochondrial proton leak: influence of membrane surface area and fatty acid composition. Am J Physiol 271:1550–1560Google Scholar
  33. Shires R, Lane NJ, Inman CBE, Lockwood AP (1994) Structural changes in the gill cells of Gammarus duebeni (Crustacea, amphipoda) under osmotic stress, with notes on microtubules in association with the septate junctions. Tissue Cell 26:767CrossRefGoogle Scholar
  34. Söderhäll K, Cerenius L (1992) Crustacean immunity. Annu Rev Fish Dis 2:3–23CrossRefGoogle Scholar
  35. Sun DF, Lv JJ, Huan PP, Gao BQ, Liu P (2018) Expression analysis of neuroparsin gene under low salinity stress in swimming crab (Portunus trituberculatus). J Fish Sci China 25:67–75 (in chinese) Google Scholar
  36. Tiu SHK, He JG, Chan SM (2007) The LvCHH-ITP gene of the shrimp (Litopenaeus vannamei) produces a widely expressed putative ion transport peptide (LvITP) for osmo-regulation. Gene 396:226–235CrossRefGoogle Scholar
  37. Watts SA, Yeh EW, Henry RP (1996) Hypoosmotic stimulation of Ornithinede carboxylase activity in the brine shrimp Artemia framiscana. J Exp Zool 274:15–22CrossRefGoogle Scholar
  38. Webster SG, Keller R, Dircksen H (2012) The CHH-superfamily of multifunctional peptide hormones controlling crustacean metabolism, osmoregulation, moulting, and reproduction. Gen Comp Endocrinol 175:217–233CrossRefGoogle Scholar
  39. Whitney JO (1974) The effect of external salinity upon lipid synthesis in the blue crab Callinectes sapidus Rathbun and in the spider crab Libinia emarginata Leech. Comp Biochem Physiol A Comp Physiol 49(3):433–440CrossRefGoogle Scholar
  40. Xu QH (2011) Gene expression profiles of the swimming crab Portunus trituberculatus exposed to salinity stress. Mar Biol 158:2161–2172CrossRefGoogle Scholar
  41. Zhang DB, Li AG (1992) Study on the limit salinity and suitable salinity of zoeal of Portunus trifasciatus. Mar Sci 16:8–10 (in chinese) Google Scholar
  42. Zhang F, Lv JJ, Liu P, Gao BQ, Li Li, Chen P (2015) Cloning and expression of chitinase under low salintty stress during molting in Portunus trituberculatus. Oceanologia et Limnologia Sinica 46:948–957 (in chinese) Google Scholar
  43. Zhou SL, Jiang NC, Lu JP, Yang WX (2001) Progress of the study on osmotic regulation in crustaceans I. the gill’s structure and function and its’ concerned factors. Donghai Mar Sci 19:45–52Google Scholar

Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  • Baoquan Gao
    • 1
    • 2
  • Dongfang Sun
    • 1
  • Jianjian Lv
    • 1
    • 2
  • Xianyun Ren
    • 1
    • 2
  • Ping Liu
    • 1
    • 2
    Email author
  • Jian Li
    • 1
    • 2
  1. 1.Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoPeople’s Republic of China
  2. 2.Laboratory for Marine Fisheries and AquacultureQingdao National Laboratory for Marine Science and TechnologyQingdaoPeople’s Republic of China

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