BioEnergy Research

, Volume 7, Issue 1, pp 192–205 | Cite as

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

  • Ruo-lin Cheng
  • Jia Feng
  • Bing-Xin Zhang
  • Yun Huang
  • Jun Cheng
  • Chuan-Xi ZhangEmail author


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.


Diatom Differential expression Freshwater Nitzschia Seawater Transcriptome 



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).

Supplementary material

12155_2013_9360_MOESM1_ESM.xls (26 kb)
Table S1 Primers used in qRT-PCR. (XLS 25 kb)
12155_2013_9360_MOESM2_ESM.xls (3.3 mb)
Table S2 Genes differentially expressed under salinity stress. (XLS 3410 kb)
12155_2013_9360_MOESM3_ESM.xls (58 kb)
Table S3 Differentially expressed genes related to C and N metabolism. (XLS 57 kb)
12155_2013_9360_Fig7_ESM.gif (52 kb)
Fig. 1

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

12155_2013_9360_MOESM4_ESM.tif (59 kb)
High resolution image (TIFF 59 kb)


  1. 1.
    Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281(5374):237–240PubMedCrossRefGoogle Scholar
  2. 2.
    Falkowski PG, Barber RT, Smetacek V (1998) Biogeochemical controls and feedbacks on ocean primary production. Science 281(5374):200–206PubMedCrossRefGoogle Scholar
  3. 3.
    Hildebrand M (2008) Diatoms, biomineralization processes, and genomics. Chem Rev 108(11):4855–4874PubMedCrossRefGoogle Scholar
  4. 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, COGoogle Scholar
  5. 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):8769–8788Google Scholar
  6. 6.
    Mann DG, Droop SJ (1996) 3. Biodiversity, biogeography and conservation of diatoms. Hydrobiologia 336(1):19–32CrossRefGoogle Scholar
  7. 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):31–41PubMedCrossRefGoogle Scholar
  8. 8.
    Huang GH, Chen F, Wei D, Zhang XW, Chen G (2010) Biodiesel production by microalgal biotechnology. Appl Energ 87(1):38–46CrossRefGoogle Scholar
  9. 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):621–639PubMedCrossRefGoogle Scholar
  10. 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):631–635CrossRefGoogle Scholar
  11. 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):467–482Google Scholar
  12. 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):223–226PubMedCrossRefGoogle Scholar
  13. 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):1737–1752PubMedCentralPubMedCrossRefGoogle Scholar
  14. 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):79–86PubMedCrossRefGoogle Scholar
  15. 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):239–244PubMedCrossRefGoogle Scholar
  16. 16.
    Dunahay TG, Jarvis EE, Roessler PG (1995) Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophila. J Phycol 31(6):1004–1012CrossRefGoogle Scholar
  17. 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):379–386CrossRefGoogle Scholar
  18. 18.
    Radakovits R, Jinkerson RE, Darzins A, Posewitz MC (2010) Genetic engineering of algae for enhanced biofuel production. Eukaryot Cell 9(4):486–501PubMedCentralPubMedCrossRefGoogle Scholar
  19. 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 29–60CrossRefGoogle Scholar
  20. 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):644–652PubMedCentralPubMedCrossRefGoogle Scholar
  21. 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):1944–1954PubMedCentralPubMedCrossRefGoogle Scholar
  22. 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–W322PubMedCentralPubMedCrossRefGoogle Scholar
  23. 23.
    Hildebrand M, Volcani BE, Gassmann W, Schroeder JI (1997) A gene family of silicon transporters. Nature 385(6618):688–689PubMedCrossRefGoogle Scholar
  24. 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):480–486PubMedCrossRefGoogle Scholar
  25. 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):822–834CrossRefGoogle Scholar
  26. 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):269–280CrossRefGoogle Scholar
  27. 27.
    Kroger N, Poulsen N (2008) Diatoms—from cell wall biogenesis to nanotechnology. Annu Rev Genet 42:83–107PubMedCrossRefGoogle Scholar
  28. 28.
    Sumper M, Kröger N (2004) Silica formation in diatoms: the function of long-chain polyamines and silaffins. J Mater Chem 14(14):2059–2065CrossRefGoogle Scholar
  29. 29.
    Poulsen N, Kröger N (2004) Silica morphogenesis by alternative processing of silaffins in the diatom Thalassiosira pseudonana. J Biol Chem 279(41):42993–42999PubMedCrossRefGoogle Scholar
  30. 30.
    Guschina IA, Harwood JL (2006) Lipids and lipid metabolism in eukaryotic algae. Prog Lipid Res 45(2):160–186PubMedCrossRefGoogle Scholar
  31. 31.
    Ohlrogge JB, Jaworski JG (1997) Regulation of fatty acid synthesis. Annu Rev Plant Biol 48(1):109–136CrossRefGoogle Scholar
  32. 32.
    Khozin-Goldberg I, Cohen Z (2011) Unraveling algal lipid metabolism: recent advances in gene identification. Biochimie 93(1SI):91–100PubMedCrossRefGoogle Scholar
  33. 33.
    Roessler PG (1990) Environmental control of glycerolipid metabolism in microalgae: commercial implications and future research directions. J Phycol 26(3):393–399CrossRefGoogle Scholar
  34. 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–D827PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Hasle GR (2004) Pseudo-nitzschia as a genus distinct from Nitzschia (Bacillariophyceae). J Phycol 30(6):1036–1039CrossRefGoogle Scholar
  36. 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):354–360PubMedCrossRefGoogle Scholar
  37. 37.
    Dagan T, Martin W (2009) Seeing green and red in diatom genomes. Science 324(5935):1651–1652PubMedCrossRefGoogle Scholar
  38. 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):1724–1726PubMedCrossRefGoogle Scholar
  39. 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):242–252PubMedCentralPubMedCrossRefGoogle Scholar
  40. 40.
    Ohlrogge JB, Somerville CR (1991) The genetics of plant lipids. Biochim Biophys Acta 1082(1):1–26PubMedCrossRefGoogle Scholar
  41. 41.
    Ohlrogge J, Browse J (1995) Lipid biosynthesis. Plant Cell 7:957–970PubMedCentralPubMedGoogle Scholar
  42. 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):6487–6492PubMedCentralPubMedCrossRefGoogle Scholar
  43. 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)Google Scholar
  44. 44.
    Coleman RA, Lee DP (2004) Enzymes of triacylglycerol synthesis and their regulation. Prog Lipid Res 43(2):134–176PubMedCrossRefGoogle Scholar
  45. 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):347–361PubMedCentralPubMedCrossRefGoogle Scholar
  46. 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):405–419PubMedCrossRefGoogle Scholar
  47. 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):1095–1102PubMedCrossRefGoogle Scholar
  48. 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):645–655CrossRefGoogle Scholar
  49. 49.
    Rea PA (2007) Plant ATP-binding cassette transporters. Annu Rev Plant Biol 58:347–375PubMedCrossRefGoogle Scholar
  50. 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):1955–1962PubMedCrossRefGoogle Scholar
  51. 51.
    Chen H, Jiang JG (2009) Osmotic responses of Dunaliella to the changes of salinity. J Cell Physiol 219(2):251–258PubMedCrossRefGoogle Scholar
  52. 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):1320–1329PubMedCentralPubMedCrossRefGoogle Scholar
  53. 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):2731–2739PubMedCentralPubMedCrossRefGoogle Scholar
  54. 54.
    Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13(9):2178–2189PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Ruo-lin Cheng
    • 1
  • Jia Feng
    • 2
  • Bing-Xin Zhang
    • 1
  • Yun Huang
    • 2
  • Jun Cheng
    • 2
  • Chuan-Xi Zhang
    • 1
    Email author
  1. 1.College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
  2. 2.State Key Laboratory of Clean Energy UtilizationZhejiang UniversityHangzhouChina

Personalised recommendations