Skip to main content

Advertisement

SpringerLink
Log in

Transcriptome and Gene Expression Analysis of an Oleaginous Diatom Under Different Salinity Conditions

  • Published:
BioEnergy Research Aims and scope Submit manuscript

Abstract

Diatoms constitute a remarkably diverse and attractive group of microalgae, serving as the main primary producers in many ecosystems and a potential source of renewable biofuel. The enhancement of lipid production in diatoms has been achieved by the optimization of culture conditions, such as temperature, salinity, and nutrient starvation. In this study, we performed Illumina sequencing and the de novo transcriptome assembly of an oleaginous diatom, Nitzschia sp., which produces up to 50 % oil by weight under defined conditions. High-quality reads were assembled into 28,117 isogenes and then subjected to BLAST alignment, Gene Ontology annotation, and KEGG Orthology annotation. The majority of genes and pathways related to cell wall formation and lipid biosynthesis were identified by these analyses. In addition, elevated salinity was found to increase the total lipid content of Nitzschia sp. For a better understanding of the molecular mechanisms regulating this phenomenon, transcriptome profiles under different conditions of salinity were compared to examine how the metabolic flux was channeled to increase the biosynthesis of triacylglycerols. As expected, a subset of genes involved in lipid biosynthesis was up-regulated under salinity stress. Meanwhile, carbon and nitrogen metabolism genes were also significantly affected, indicating a diversion of metabolic pathways. The data we generated here enrich the genomic resources available for non-model algae and provide insights into the mechanisms of lipid accumulation in microalgae.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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
Fig. 5
Fig. 6

We’re sorry, something doesn't seem to be working properly.

Please try refreshing the page. If that doesn't work, please contact support so we can address the problem.

References

  1. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281(5374):237–240

    Article  CAS  PubMed  Google Scholar 

  2. Falkowski PG, Barber RT, Smetacek V (1998) Biogeochemical controls and feedbacks on ocean primary production. Science 281(5374):200–206

    Article  CAS  PubMed  Google Scholar 

  3. Hildebrand M (2008) Diatoms, biomineralization processes, and genomics. Chem Rev 108(11):4855–4874

    Article  CAS  PubMed  Google Scholar 

  4. Sheehan J, Dunahay T, Benemann J, Roessler P (1998) A look back at the US Department of Energy’s aquatic species program: biodiesel from algae. 328th ed. National Renewable Energy Laboratory, Golden, CO

  5. Ramahandra TV, Mahpatra DM, Gordon R (2009) Milking diatoms for sustainable energy: biochemical engineering versus gasoline-secreting diatom solar panels. Ind Eng Chem Res 48(19):8769–8788

    Google Scholar 

  6. Mann DG, Droop SJ (1996) 3. Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336(1):19–32

    Article  Google Scholar 

  7. Courchesne NMD, Parisien A, Wang B, Lan CQ (2009) Enhancement of lipid production using biochemical, genetic and transcription factor engineering approaches. J Biotechnol 141(1):31–41

    Article  CAS  PubMed  Google Scholar 

  8. Huang GH, Chen F, Wei D, Zhang XW, Chen G (2010) Biodiesel production by microalgal biotechnology. Appl Energ 87(1):38–46

    Article  CAS  Google Scholar 

  9. Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, Seibert M et al (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J 54(4):621–639

    Article  CAS  PubMed  Google Scholar 

  10. Illman AM, Scragg AH, Shales SW (2000) Increase in Chlorella strains calorific values when grown in low nitrogen medium. Enzyme Microb Tech 27(8):631–635

    Article  CAS  Google Scholar 

  11. Floreto E, Teshima S (1998) The fatty acid composition of seaweeds exposed to different levels of light intensity and salinity. Bot Mar 41(1–6):467–482

    CAS  Google Scholar 

  12. Takagi M, Yoshida T (2006) Effect of salt concentration on intracellular accumulation of lipids and triacylglyceride in marine microalgae Dunaliella cells. J Biosci Bioeng 101(3):223–226

    Article  CAS  PubMed  Google Scholar 

  13. Miller R, Wu GX, Deshpande RR, Vieler A, Gartner K, Li XB et al (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol 154(4):1737–1752

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH et al (2004) The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306(5693):79–86

    Article  CAS  PubMed  Google Scholar 

  15. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A et al (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456(7219):239–244

    Article  CAS  PubMed  Google Scholar 

  16. Dunahay TG, Jarvis EE, Roessler PG (1995) Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophila. J Phycol 31(6):1004–1012

    Article  CAS  Google Scholar 

  17. Zaslavskaia LA, Lippmeier JC, Kroth PG, Grossman AR, Apt KE (2000) Transformation of the diatom Phaeodactylum tricornutum (Bacillariophyceae) with a variety of selectable marker and reporter genes. J Phycol 36(2):379–386

    Article  CAS  Google Scholar 

  18. Radakovits R, Jinkerson RE, Darzins A, Posewitz MC (2010) Genetic engineering of algae for enhanced biofuel production. Eukaryot Cell 9(4):486–501

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Guillard RL (1975) Culture of phytoplankton for feeding marine invertebrates. In: Smith WL, Chanley MH (eds) Culture of marine invertebrate animals. Plenum, New York, pp 29–60

    Chapter  Google Scholar 

  20. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res 18(12):1944–1954

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S et al (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 39(suppl 2):W316–W322

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  23. Hildebrand M, Volcani BE, Gassmann W, Schroeder JI (1997) A gene family of silicon transporters. Nature 385(6618):688–689

    Article  CAS  PubMed  Google Scholar 

  24. Hildebrand M, Dahlin K, Volcani BE (1998) Characterization of a silicon transporter gene family in Cylindrotheca fusiformis: sequences, expression analysis, and identification of homologs in other diatoms. Mol Gen Genet 260(5):480–486

    Article  CAS  PubMed  Google Scholar 

  25. Thamatrakoln K, Alverson AJ, Hildebrand M (2006) Comparative sequence analysis of diatom silicon transporters: toward a mechanistic model of silicon transport. J Phycol 42(4):822–834

    Article  CAS  Google Scholar 

  26. Sherbakova TA, Masyukova YA, Safonova TA, Petrova DP, Vereshagin AL, Minaeva TV et al (2005) Conserved motif CMLD in silicic acid transport proteins of diatoms. Mol Biol 39(2):269–280

    Article  CAS  Google Scholar 

  27. Kroger N, Poulsen N (2008) Diatoms—from cell wall biogenesis to nanotechnology. Annu Rev Genet 42:83–107

    Article  CAS  PubMed  Google Scholar 

  28. Sumper M, Kröger N (2004) Silica formation in diatoms: the function of long-chain polyamines and silaffins. J Mater Chem 14(14):2059–2065

    Article  CAS  Google Scholar 

  29. Poulsen N, Kröger N (2004) Silica morphogenesis by alternative processing of silaffins in the diatom Thalassiosira pseudonana. J Biol Chem 279(41):42993–42999

    Article  CAS  PubMed  Google Scholar 

  30. Guschina IA, Harwood JL (2006) Lipids and lipid metabolism in eukaryotic algae. Prog Lipid Res 45(2):160–186

    Article  CAS  PubMed  Google Scholar 

  31. Ohlrogge JB, Jaworski JG (1997) Regulation of fatty acid synthesis. Annu Rev Plant Biol 48(1):109–136

    Article  CAS  Google Scholar 

  32. Khozin-Goldberg I, Cohen Z (2011) Unraveling algal lipid metabolism: recent advances in gene identification. Biochimie 93(1SI):91–100

    Article  CAS  PubMed  Google Scholar 

  33. Roessler PG (1990) Environmental control of glycerolipid metabolism in microalgae: commercial implications and future research directions. J Phycol 26(3):393–399

    Article  CAS  Google Scholar 

  34. Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LGG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38(suppl 1):D822–D827

    Article  PubMed Central  PubMed  Google Scholar 

  35. Hasle GR (2004) Pseudo-nitzschia as a genus distinct from Nitzschia (Bacillariophyceae). J Phycol 30(6):1036–1039

    Article  Google Scholar 

  36. Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O et al (2004) The evolution of modern eukaryotic phytoplankton. Science 305(5682):354–360

    Article  CAS  PubMed  Google Scholar 

  37. Dagan T, Martin W (2009) Seeing green and red in diatom genomes. Science 324(5935):1651–1652

    Article  CAS  PubMed  Google Scholar 

  38. Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324(5935):1724–1726

    Article  CAS  PubMed  Google Scholar 

  39. Riekhof WR, Sears BB, Benning C (2005) Annotation of genes involved in glycerolipid biosynthesis in Chlamydomonas reinhardtii: discovery of the betaine lipid synthase BTA1Cr. Eukaryot Cell 4(2):242–252

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Ohlrogge JB, Somerville CR (1991) The genetics of plant lipids. Biochim Biophys Acta 1082(1):1–26

    Article  CAS  PubMed  Google Scholar 

  41. Ohlrogge J, Browse J (1995) Lipid biosynthesis. Plant Cell 7:957–970

    CAS  PubMed Central  PubMed  Google Scholar 

  42. Dahlqvist A, Ståhl U, Lenman M, Banas A, Lee M, Sandager L et al (2000) Phospholipid: diacylglycerol acyltransferase: an enzyme that catalyzes the acyl-CoA-independent formation of triacylglycerol in yeast and plants. Proc Natl Acad Sci USA 97(12):6487–6492

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J (2011) Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 12(148)

  44. Coleman RA, Lee DP (2004) Enzymes of triacylglycerol synthesis and their regulation. Prog Lipid Res 43(2):134–176

    Article  CAS  PubMed  Google Scholar 

  45. Schwender J, Ohlrogge JB (2002) Probing in vivo metabolism by stable isotope labeling of storage lipids and proteins in developing Brassica napus embryos. Plant Physiol 130(1):347–361

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  46. Baud S, Wuillème S, Dubreucq B, De Almeida A, Vuagnat C, Lepiniec L et al (2007) Function of plastidial pyruvate kinases in seeds of Arabidopsis thaliana. Plant J 52(3):405–419

    Article  CAS  PubMed  Google Scholar 

  47. Yoshiba Y, Kiyosue T, Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K (1997) Regulation of levels of proline as an osmolyte in plants under water stress. Plant Cell Physiol 38(10):1095–1102

    Article  CAS  PubMed  Google Scholar 

  48. Dickson D, Kirst GO (2006) Osmotic adjustment in marine eukaryotic algae: the role of inorganic ions, quaternary ammonium, tertiary sulphonium and carbohydrate solutes. New Phytol 106(4):645–655

    Article  Google Scholar 

  49. Rea PA (2007) Plant ATP-binding cassette transporters. Annu Rev Plant Biol 58:347–375

    Article  CAS  PubMed  Google Scholar 

  50. Tausz M, Šircelj H, Grill D (2004) The glutathione system as a stress marker in plant ecophysiology: is a stress-response concept valid? J Exp Bot 55(404):1955–1962

    Article  CAS  PubMed  Google Scholar 

  51. Chen H, Jiang JG (2009) Osmotic responses of Dunaliella to the changes of salinity. J Cell Physiol 219(2):251–258

    Article  CAS  PubMed  Google Scholar 

  52. Azachi M, Sadka A, Fisher M, Goldshlag P, Gokhman I, Zamir A (2002) Salt induction of fatty acid elongase and membrane lipid modifications in the extreme halotolerant alga Dunaliella salina. Plant Physiol 129(3):1320–1329

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  53. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  54. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13(9):2178–2189

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgment

This project was supported by the National High Technology R&D Program of China (2012AA050101), National Natural Science Foundation of China (51176163), and Key Natural Science Foundation of Zhejiang Province (Z1090532).

Author information

Authors and Affiliations

  1. College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Ruo-lin Cheng, Bing-Xin Zhang & Chuan-Xi Zhang

  2. State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China

    Jia Feng, Yun Huang & Jun Cheng

Authors
  1. Ruo-lin Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jia Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bing-Xin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yun Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jun Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chuan-Xi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chuan-Xi Zhang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table S1

Primers used in qRT-PCR. (XLS 25 kb)

Table S2

Genes differentially expressed under salinity stress. (XLS 3410 kb)

Table S3

Differentially expressed genes related to C and N metabolism. (XLS 57 kb)

Fig. 1

Sequence length distribution of the Nitzschia sp. transcriptome assembly. (GIF 51 kb)

High resolution image (TIFF 59 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cheng, Rl., Feng, J., Zhang, BX. et al. Transcriptome and Gene Expression Analysis of an Oleaginous Diatom Under Different Salinity Conditions. Bioenerg. Res. 7, 192–205 (2014). https://doi.org/10.1007/s12155-013-9360-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12155-013-9360-1

Keywords

Search

Navigation