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De Novo Sequencing and Global Transcriptome Analysis of Nannochloropsis sp. (Eustigmatophyceae) Following Nitrogen Starvation

Abstract

Nannochloropsis sp. is an economically and nutritionally important microalga. Recently it has been demonstrated that Nannochloropsis sp. has significant potential for biofuel production. To determine the mechanisms of lipid formation and accumulation during nitrogen starvation, a transcriptomic study was performed to compare gene expression during growth with and without nitrogen. Digital expression analysis identified 1,855 differentially expressed genes between cells grown under nitrogen-replete and nitrogen-deprived conditions; this provided novel insights into the molecular mechanisms of lipid formation by Nannochloropsis sp. under stress. As expected, nitrogen deprivation induced genes involved in nitrogen metabolism and lipid biosynthesis. Although the chlorophyll content decreased following nitrogen deprivation, a subset of genes putatively encoding light-harvesting complex (LHC) proteins were upregulated. These upregulated LHCs may play a role on photoprotection. The sequence data were confirmed using reverse transcription polymerase chain reaction (RT-PCR) and quantitative real-time RT-PCR. The expressions of a number of genes involved in acetyl-CoA metabolism were also affected under nitrogen-deprived stress, which may change fatty acids indirectly. Overall, we found low gene expression levels for fatty acid synthesis, suggesting that the buildup of precursors for the acetyl-CoA carboxylases may play a more significant role in TAG synthesis compared with the actual enzyme levels of acetyl-CoA carboxylases per se. The changes in transcript abundance in Nannochloropsis sp. following nitrogen deprivation provided a potential source for exploration of molecular mechanisms of lipid formation and accumulation. Furthermore, a set of simple sequence repeat motifs were identified from the expressed sequence tags, which provide useful genetic markers for further genetic analysis.

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Acknowledgments

The authors thank the Beijing Institutes of Life Science, Chinese Academy of Sciences (BIOLS), for kind assistance in bioinformatic analysis. This work was supported by Shandong Science and Technology plan project (2011GHY11528), the Specialized Fund for the Basic Research Operating Expenses Program (20603022012004), National Natural Science Foundation of China (41176153, 31000135,40972162), Natural Science Foundation of Shandong Province (2009ZRA02075), Qingdao Municipal Science and Technology plan project (11-3-1-5-hy, 11-2-4-3-(5)-jch), and National Marine Public Welfare Research Project (200805069).

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Correspondence to Naihao Ye.

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Chengwei Liang and Shaona Cao contributed equally to this work.

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Additional File 1

The primers used in the qPCR. (XLS 28 kb)

Additional File 2

The total information of Unigenes. This file contains every identified gene, its annotation based on the public database and its change in expression between the two different conditions. (XLS 7,739 kb)

Additional File 3

Pathway based on the KEGG. The file includes the pathways in which the differently expressed gene involved. (XLS 105 kb)

Additional File 4

SSR markers and designed primers. SSR markers were identified based on the EST sequences and primers were designed based the SSRs. (XLS 1,631 kb)

Additional File 5

All the EST sequence data. The file can be read by the softwares such as Utraedit, Dnaman, NotePad et al. (SEQ 9,945 kb)

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Liang, C., Cao, S., Zhang, X. et al. De Novo Sequencing and Global Transcriptome Analysis of Nannochloropsis sp. (Eustigmatophyceae) Following Nitrogen Starvation. Bioenerg. Res. 6, 494–505 (2013). https://doi.org/10.1007/s12155-012-9269-0

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Keywords

  • Nannochloropsis sp.
  • Transcriptome
  • Nitrogen starvation