Skip to main content
SpringerLink
Log in

Comparative morphological, physiological, biochemical and genomic studies reveal novel genes of Dunaliella bioculata and D. quartolecta in response to salt stress

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

Salinity is an essential abiotic stress in plants. Dunaliella is a genus of high-salt-tolerant microalgae. The present study aimed to compare the characterizations of D. bioculata and D. quartolecta at different levels and investigate novel genes response to salt stress.

Methods and results

High chlorophyll contents were detected in D. bioculata on the 35th d of salt stress, while high lipid and carotenoid contents were detected in D. quartolecta via morphological and biochemical analyses. Physiological analysis showed that D. quartolecta cells had a smaller increase in osmotic potential, a smaller decrease in the Na+/K+ ratio and photochemical efficiency (Fv/Fm), and a lower relative conductivity than D. bioculata cells. The genomic lengths of D. quartolecta and D. bioculata were 396,013,629 bp (scaffold N50 = 1954 bp) and 427,667,563 bp (scaffold N50 = 3093 bp) via high-throughput sequencing and de novo assembly, respectively. Altogether, 25,751 and 26,620 genes were predicted in their genomes by annotation analysis with various biodatabases. The D. bioculata genome showed more segmental duplication events via collinearity analysis. More single nucleotide polymorphisms and insertion-deletion variants were detected in the D. bioculata genome. Both algae, which showed a close phylogenetic relationship, may undergo positive selection via bioinformatics analysis. A total of 382 and 85 novel genes were screened in D. bioculata and D. quartolecta, with 138 and 51 enriched KEGG pathways, respectively. Unlike the novel genes adh1, hprA and serA, the relative expression of livF and phbB in D. bioculata was markedly downregulated as salinity increased, as determined by qPCR analysis. The relative expression of leuB, asd, pstC and proA in D. quartolecta was markedly upregulated with the same salinity increase.

Conclusion

Dunaliella quartolecta is more halophilic than D. bioculata, with more effective responses to high salt stress based on the multiphase comparative data.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Availability of data and materials

The raw genome sequencing datasets in this study are available from the NCBI Sequence Read Archive (SRA) database with the accession numbers SRR12329620 and SRR12329789. The authors declare that all the other data supporting the findings of this study are available within the article and its supplementary files.

References

  1. Ścieszka S, Klewicka E (2019) Algae in food: a general review. Crit Rev Food Sci Nutr 59(21):3538–3547. https://doi.org/10.1080/10408398.2018.1496319

    Article  CAS  PubMed  Google Scholar 

  2. Kim JH, Lee JE, Kim KH et al (2018) Beneficial effects of marine algae-derived carbohydrates for skin health. Mar Drugs 16(11):459. https://doi.org/10.3390/md16110459

    Article  CAS  PubMed Central  Google Scholar 

  3. Lenka SK, Carbonaro N, Park R et al (2016) Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis. Biotechnol Adv 34:1046–1063

    Article  CAS  PubMed  Google Scholar 

  4. Mao X, Zhang Y, Wang X et al (2020) Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study. Biotechnol Biofuels 13:73. https://doi.org/10.1186/s13068-020-01714-y

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Avron M (1986) The osmotic components of halotolerant algae. Trends Biochem Sci 11(1):5–6. https://doi.org/10.1016/0968-0004(86)90200-8

    Article  CAS  Google Scholar 

  6. Glöckner G, Rosenthal A, Valentin K (2000) The structure and gene repertoire of an ancient red algal plastid genome. J Mol Evol 51(4):382–390. https://doi.org/10.1007/s002390010101

    Article  PubMed  Google Scholar 

  7. Kim GY, Heo J, Kim HS et al (2017) Bicarbonate-based cultivation of Dunaliella salina for enhancing carbon utilization efficiency. Biores Technol 237:72–77. https://doi.org/10.1016/j.biortech.2017.04.009

    Article  CAS  Google Scholar 

  8. Oren A (2014) The ecology of Dunaliella in high-salt environments. J Biol Res (Thessalon) 21(1):23. https://doi.org/10.1186/s40709-014-0023-y(In Chinese)

    Article  Google Scholar 

  9. Wang T, Feng J, Xie SL (2014) Effects on culture conditions for β-carotene contents of Dunaliella sp. Sci Technol Food Ind 24:177–181. https://doi.org/10.13386/j.issn1002-0306.2014.24.029

  10. Sadka A, Himmelhoch S, Zamir A (1991) A 150 kilodalton cell surface protein is induced by salt in the halotolerant green alga Dunaliella salina. Plant Physiol 95(3):822–831. https://doi.org/10.1104/pp.95.3.822

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Chen H, Jiang JG (2009) Osmotic responses of Dunaliella to the changes of salinity. J Cell Physiol 219(2):251–258. https://doi.org/10.1002/jcp.21715

    Article  CAS  PubMed  Google Scholar 

  12. Liang MH, Jiang JG (2017) Analysis of carotenogenic genes promoters and WRKY transcription factors in response to salt stress in Dunaliella bardawil. Sci Rep 7:37025. https://doi.org/10.1038/srep37025

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Sui Y, Vlaeminck SE (2020) Dunaliella microalgae for nutritional protein: an undervalued asset. Trends Biotechnol 38(1):10–12. https://doi.org/10.1016/j.tibtech.2019.07.011

    Article  CAS  PubMed  Google Scholar 

  14. Monte J, Ribeiro C, Parreira C et al (2020) Biorefinery of Dunaliella salina: sustainable recovery of carotenoids, polar lipids and glycerol. Biores Technol 297:122509. https://doi.org/10.1016/j.biortech.2019.122509

    Article  CAS  Google Scholar 

  15. Xu Y, Ibrahim IM, Wosu CI et al (2018) Potential of new isolates of Dunaliella salina for natural β-carotene production. Biology 7(1):14. https://doi.org/10.3390/biology7010014

    Article  CAS  PubMed Central  Google Scholar 

  16. Bohn T, Desmarchelier C, El SN et al (2019) β-Carotene in the human body: metabolic bioactivation pathways-from digestion to tissue distribution and excretion. Proc Nutr Soc 78(1):68–87. https://doi.org/10.1017/S0029665118002641

    Article  CAS  PubMed  Google Scholar 

  17. Kim D, Lim JW, Kim H (2019) β-Carotene inhibits expression of c-Myc and cyclin E in Helicobacter pylori-infected gastric epithelial cells. J Cancer Prev 24(3):192–196. https://doi.org/10.15430/JCP.2019.24.3.192

  18. Raja R, Hemaiswarya S, Rengasamy R (2007) Exploitation of Dunaliella for beta-carotene production. Appl Microbiol Biotechnol 74(3):517–523. https://doi.org/10.1007/s00253-006-0777-8

    Article  CAS  PubMed  Google Scholar 

  19. Liang MH, Lu Y, Chen HH (2017) The salt-regulated element in the promoter of lycopene β-cyclase gene confers a salt regulatory pattern in carotenogenesis of Dunaliella bardawil. Environ Microbiol 19(3):982–989. https://doi.org/10.1111/1462-2920.13539.18

    Article  CAS  PubMed  Google Scholar 

  20. Li J, Lu Y, Xue L et al (2010) A structurally novel salt-regulated promoter of duplicated carbonic anhydrase gene 1 from Dunaliella salina. Mol Biol Rep 37(2):1143–1154. https://doi.org/10.1007/s11033-009-9901-z

    Article  CAS  PubMed  Google Scholar 

  21. Xing Z, Gao X, Wang M et al (2020) Identification of salt-responsive genes using transcriptome analysis in Dunaliella viridis. J Appl Phycol 32(5):2875–2887. https://doi.org/10.1007/s10811-020-02142-z

    Article  CAS  Google Scholar 

  22. Santín-Montanyá I, Sandín-España P, García Baudín JM et al (2007) Optimal growth of Dunaliella primolecta in axenic conditions to assay herbicides. Chemosphere 66(7):1315–1322. https://doi.org/10.1016/j.chemosphere.2006.07.019

    Article  CAS  PubMed  Google Scholar 

  23. Khan AK, Kausar H, Jaferi SS et al (2020) An insight into the algal evolution and genomics. Biomolecules 10(11):1524. https://doi.org/10.3390/biom10111524

    Article  CAS  PubMed Central  Google Scholar 

  24. Polle JEW, Barry K, Cushman J et al (2017) Draft nuclear genome sequence of the halophilic and beta-carotene-accumulating green alga Dunaliella salina strain CCAP19/18. Genome Announc 5(43):e01105-e1117. https://doi.org/10.1128/genomeA.01105-17

    Article  PubMed Central  PubMed  Google Scholar 

  25. Wang T, Feng J, Xie SL (2014) Effects on culture conditions for β-carotene contents of Dunaliella sp. Sci Technol Food Ind 35(24):177–181. https://doi.org/10.13386/j.issn1002-0306.2014.24.029(In Chinese)

    Article  CAS  Google Scholar 

  26. Yin XG (2019) Physiological and biochemical and phylogentic studies of different strains of Dunaliella. Shanxi University, Taiyuan

    Google Scholar 

  27. Gao F, Nan F, Feng J et al (2021) Transcriptome profi le of Dunaliella salina in Yuncheng Salt Lake reveals salt-stress-related genes under different salinity stresses. J Oceanol Limnol. https://doi.org/10.1007/s00343-021-0164-4

    Article  Google Scholar 

  28. Nayaka S, Upreti DK (2008) Diversity and ecophysiology of lichens in Schirmacher Oasis, Antarctica. Ministry of Earth Sciences. Technical Publication No. 26, pp 305–326. https://www.researchgate.net/publication/342242589_Diversity_and_ecophysiology_of_lichens_in_Schirmacher_Oasis_Antarctica

  29. Munns R, Wallace PA, Teakle NL et al (2010) Measuring soluble ion concentrations (Na(+), K(+), Cl(-)) in salt-treated plants. Methods Mol Biol 639:371–382. https://doi.org/10.1007/978-1-60761-702-0_23

    Article  CAS  PubMed  Google Scholar 

  30. Li G, Wang G, Song L et al (2002) Lipid peroxidation in microalgae cells under simulated microgravity. Space Med Med Eng (Beijing) 15(4):270–272. https://doi.org/10.1007/s11769-002-0038-4

    Article  Google Scholar 

  31. Yu Z, Zhang T, Zhu Y (2020) Whole-genome re-sequencing and transcriptome reveal cadmium tolerance related genes and pathways in Chlamydomonas reinhardtii. Ecotoxicol Environ Saf 191:110231. https://doi.org/10.1016/j.ecoenv.2020.110231

    Article  CAS  PubMed  Google Scholar 

  32. Mera R, Torres E, Abalde J (2016) Effects of sodium sulfate on the freshwater microalga Chlamydomonas moewusii: implications for the optimization of algal culture media. J Phycol 52(1):75–88. https://doi.org/10.1111/jpy.12367

    Article  CAS  PubMed  Google Scholar 

  33. Gao Y (2019) Effects of nitrogen deprivation and nutrition way on the lipid accumulation of Parachlorella kessleri TY. Thesis for doctor’s degree, Shanxi University, Taiyuan, 2019 (in Chinese). https://doi.org/10.27284/d.cnki.gsxiu.2019.001530

  34. Yu Z, Zhang T, Hao R et al (2019) Sensitivity of Chlamydomonas reinhardtii to cadmium stress is associated with phototaxis. Environ Sci Process Impacts 21:1011–1020. https://doi.org/10.1039/c9em00013e

    Article  CAS  PubMed  Google Scholar 

  35. Xie Y, Wu G, Tang J et al (2014) SOAP denovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30(12):1660–1666. https://doi.org/10.1093/bioinformatics/btu077

    Article  CAS  PubMed  Google Scholar 

  36. Simpson JT, Wong K, Jackman SD et al (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117–1123. https://doi.org/10.1101/gr.089532.108

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  37. Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform. https://doi.org/10.1002/0471250953.bi0410s25

    Article  Google Scholar 

  38. Stanke M, Keller O, Gunduz I et al (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435–W439. https://doi.org/10.1093/nar/gkl200

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60. https://doi.org/10.1038/nmeth.3176

    Article  CAS  PubMed  Google Scholar 

  40. Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47(1):309–314. https://doi.org/10.1093/nar/gky1085

    Article  CAS  Google Scholar 

  41. Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16(1):157. https://doi.org/10.1186/s13059-015-0721-2

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  42. Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44(W1):W242-245. https://doi.org/10.1093/nar/gkw290

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  44. Narasimhan V, Danecek P, Scally A et al (2016) BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32(11):1749–1751. https://doi.org/10.1093/bioinformatics/btw044

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  45. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5):589–595. https://doi.org/10.1093/bioinformatics/btp698

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Wang Y, Tang H, Debarry JD et al (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40(7):e49. https://doi.org/10.1093/nar/gkr1293

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Husseneder C, Mcgregor C, Lang RP (2012) Transcriptome profiling of female alates and egg-laying queens of the Formosan subterranean termite. Compar Biochem Physiol Part D 7(1):14–27. https://doi.org/10.1016/j.cbd.2011.10.002

    Article  CAS  Google Scholar 

  48. Wang W, Xing L, Xu K et al (2020) Salt stress-induced H2O2 and Ca2+ mediate K+/Na+ homeostasis in Pyropia haitanensis. J Appl Phycol 32(6):1–12. https://doi.org/10.1007/s10811-020-02284-0

    Article  CAS  Google Scholar 

  49. Spielman SJ, Wilke CO (2015) The relationship between dN/dS and scaled selection coefficients. Mol Biol Evol 32(4):1097–1108. https://doi.org/10.1093/molbev/msv003

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  50. Ma L, Zhang H, Sun L et al (2012) NADPH oxidase AtrbohD and AtrbohF function in ROS-dependent regulation of Na+/K+ homeostasis in Arabidopsis under salt stress. J Exp Bot 63(1):305–317. https://doi.org/10.1093/jxb/err280

    Article  CAS  PubMed  Google Scholar 

  51. Li L, Zhang X, He N et al (2019) Transcriptome profiling of the salt-stress response in the halophytic green alga Dunaliella salina. Plant Mol Biol Report 37(5):421–435. https://doi.org/10.1007/s11105-019-01168-z

    Article  CAS  Google Scholar 

  52. Pick U, Zarka A, Boussiba S et al (2019) A hypothesis about the origin of carotenoid lipid droplets in the green algae Dunaliella and Haematococcus. Planta 249(1):31–47. https://doi.org/10.1007/s00425-018-3050-3

    Article  CAS  PubMed  Google Scholar 

  53. Hashimoto H, Uragami C, Cogdell RJ (2016) Carotenoids and photosynthesis. Subcell Biochem 79:111–139. https://doi.org/10.1007/978-3-319-39126-7_4

    Article  CAS  PubMed  Google Scholar 

  54. Sudhir PR, Pogoryelov D, Kovacs L et al (2005) The effects of salt stress on photosynthetic electron transport and thylakoid membrane proteins in the cyanobacterium Spirulina platensis. J Biochem Mol Biol 38(4):481–485. https://doi.org/10.5483/bmbrep.2005.38.4.481

    Article  CAS  PubMed  Google Scholar 

  55. Chen H, Lu Y, Jiang JG (2012) Comparative analysis on the key enzymes of the glycerol cycle metabolic pathway in Dunaliella salina under osmotic stresses. PLoS ONE 7(6):e37578. https://doi.org/10.1371/journal.pone.0037578

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  56. Takagi M, Karseno YT (2006) Effect of salt concentration on intracellular accumulation of lipids and triacylglyceridein marine microalgae Dunaliella cells. J Biosci Bioeng 101(3):223–226. https://doi.org/10.1263/jbb.101.223

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Vikas Narang (Editage) and for editorial assistance with the English. Additionally, the authors are thankful to all members at the Institute of Hydrobiology, Chinese Academy of Sciences and BGI for supporting algae strain identification and genome sequencing.

Funding

This work was supported by the National Natural Science Foundation of China (Grant No. 31670208), the Applied Basic Research Programs of Shanxi Province of China (Grant No. 201801D221242), Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi of China (Grant No. 2019L0041) and the Shanxi “1331 Project”. Xie S., the corresponding author, was supported by the National Natural Science Foundation of China (Grant No. 41871037) and the Shanxi “1331 Project”. Gao F., the first author, was supported by the Applied Basic Research Programs of Shanxi Province of China and Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi of China.

Author information

Authors and Affiliations

  1. School of Life Science, Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, No. 92 Wucheng Road, Taiyuan, 030006, China

    Fan Gao, Fangru Nan, Jia Feng, Junping Lv, Qi Liu, Xudong Liu & Shulian Xie

Authors
  1. Fan Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fangru Nan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jia Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Junping Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qi Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xudong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Shulian Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

FG performed the experiments, analyzed the data and cowrote the manuscript; FN, JF, JL, QL and XL analyzed the data; SX supervised the project and revised the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Shulian Xie.

Ethics declarations

Conflict of interest

The authors declare no conflicts of interest.

Ethical approval

All algae sampling procedures in this study were in accordance with the guidelines for the care and use of laboratory plants of Shanxi University, and samples were obtained from CCAP (UK) and UTEX (USA) with their permission.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gao, F., Nan, F., Feng, J. et al. Comparative morphological, physiological, biochemical and genomic studies reveal novel genes of Dunaliella bioculata and D. quartolecta in response to salt stress. Mol Biol Rep 49, 1749–1761 (2022). https://doi.org/10.1007/s11033-021-06984-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-021-06984-9

Keywords

Search

Navigation