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On-line Access: 2017-10-05

Received: 2017-02-21

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Crosschecked: 2017-09-15

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 ORCID:

Ling Hong

http://orcid.org/0000-0001-9328-3369

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Journal of Zhejiang University SCIENCE B 2017 Vol.18 No.10 P.833-844

http://doi.org/10.1631/jzus.B1700088


Transcriptome sequencing and annotation of the halophytic microalga Dunaliella salina


Author(s):  Ling Hong, Jun-li Liu, Samira Z. Midoun, Philip C. Miller

Affiliation(s):  Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; more

Corresponding email(s):   lhong@mail.hust.edu.cn, pcmiller@eng.ucsd.edu

Key Words:  Dunaliella salina, Transcriptome profile, Metabolic processes and adjustment, Regulatory metabolism, Salt stress


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Ling Hong, Jun-li Liu, Samira Z. Midoun, Philip C. Miller. Transcriptome sequencing and annotation of the halophytic microalga Dunaliella salina[J]. Journal of Zhejiang University Science B, 2017, 18(10): 833-844.

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Abstract: 
The unicellular green alga Dunaliella salina is well adapted to salt stress and contains compounds (including β-carotene and vitamins) with potential commercial value. A large transcriptome database of D. salina during the adjustment, exponential and stationary growth phases was generated using a high throughput sequencing platform. We characterized the metabolic processes in D. salina with a focus on valuable metabolites, with the aim of manipulating D. salina to achieve greater economic value in large-scale production through a bioengineering strategy. Gene expression profiles under salt stress verified using quantitative polymerase chain reaction (qPCR) implied that salt can regulate the expression of key genes. This study generated a substantial fraction of D. salina transcriptional sequences for the entire growth cycle, providing a basis for the discovery of novel genes. This first full-scale transcriptome study of D. salina establishes a foundation for further comparative genomic studies.

盐生海藻杜氏盐藻的转录组测序以及注释

目的:解析杜氏盐藻代谢过程,主要关注盐胁迫下累积的代谢物(渗透平衡产物、多胺和类胡萝卜素)的代谢。
创新点:本研究通过高通量测序产生了大量来自杜氏盐藻整个生长周期的转录组数据,描述了杜氏盐藻在盐胁迫下累积的渗透平衡产物、多胺和类胡萝卜素的代谢过程。另外通过该手段也进一步分析了盐胁迫处理下,抑制精胺合成底物的供应可能会缓解盐藻增殖对胡萝卜素含量的影响。
方法:以来自3个不同生长时期的杜氏盐藻为材料,进行大规模转录组测序。在转录组功能注释的基础上,预测了杜氏盐藻盐胁迫下累积的渗透平衡产物(图3)、多胺(图4)和类胡萝卜素(图5)的代谢路径。利用相对定量聚合酶链反应(qPCR)技术构建了相关代谢路径中关键基因的表达谱(图6)。
结论:通过杜氏盐藻转录组测序共获取了39 820条单一序列。在功能注释和聚类分析的基础上预测了杜氏盐藻盐胁迫下累积的渗透平衡产物(甘油和脯氨酸)、多胺以及类胡萝卜素的代谢路径。相关代谢途径的关键酶的表达谱分析,说明盐能够调节甘油、脯氨酸以及多胺的代谢过程。抑制精胺合成底物的供应可能会缓解盐藻增殖对胡萝卜素含量的影响。

关键词:杜氏盐藻;转录谱;代谢过程与调控;调节机制;盐胁迫

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1]Alkayala, F., Albionb, R.L., Tillettb, R.L., et al., 2010. Expressed sequence tag (EST) profiling in hyper saline shocked Dunaliella salina reveals high expression of protein synthetic apparatus components. Plant Sci., 179(5):437-449.

[2]Bradbury, L.M.T., Shumskaya, M., Tzfadia, O., et al., 2012. Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms. Proc. Natl. Acad. Sci. USA, 109:E1888-E1897.

[3]Brewster, J.L., Gustin, M.C., 2014. Hog1: 20 years of discovery and impact. Sci. Signal, 7(343):re7.

[4]Cai, M., He, L.H., Yu, T.Y., 2013. Molecular clone and expression of a NAD+-dependent glycerol-3-phosphate dehydrogenase isozyme gene from the halotolerant alga Dunaliella salina. PLoS ONE, 8(4):e62287.

[5]Chen, H., Jiang, J., 2009. Osmotic responses of Dunaliella to the changes of salinity. J. Cell Physiol., 219(2):251-258.

[6]Chen, H., Lao, Y.M., Jiang, J.G., 2011. Effects of salinities on the gene expression of a (NAD+)-dependent glycerol-3-phosphate dehydrogenase in Dunaliella salina. Sci. Total Environ., 409(7):1291-1297.

[7]Chen, H., Lu, Y., Jiang, J.G., 2012. Comparative analysis on the key enzymes of the glycerol cycle metabolic pathway in Dunaliella salina under osmotic stresses. PLoS ONE, 7(6):e37578.

[8]Conesa, A., Götz, S., García-Gomez, J.M., et al., 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3674-3676.

[9]Couso, I., Vila, M., Rodriguez, H., et al., 2011. Overexpression of an exogenous phytoene synthase gene in the unicellular alga Chlamydomonas reinhardtii leads to an increase in the content of carotenoids. Biotechnol. Prog., 27(1):54-60.

[10]Deng, G., Liang, J., Xu, D., et al., 2013. The relationship between proline content, the expression level of P5CS (Δ1-pyrroline-5-carboxylate synthetase), and drought tolerance in tibetan hulless barley (Hordeum vulgare var. nudum). Russ. J. Plant Physiol., 60(5):693-700.

[11]Ferriols, V.M.E.N., Yaginuma, R., Adachi, M., et al., 2015. Cloning and characterization of farnesyl pyrophosphate synthase from the highly branched isoprenoid producing diatom Rhizosolenia setigera. Sci. Rep., 5:10246.

[12]García, F., Freile-Pelegrin, Y., Robledo, D., 2007. Physiological characterization of Dunaliella sp. (Chlorophyta, Volvocales) from Yucatan, Mexico. Bioresour. Technol., 98(7):1359-1365.

[13]Goyal, A., 2007a. Osmoregulation in Dunaliella, part I: effects of osmotic stress on photosynthesis, dark respiration and glycerol metabolism in Dunaliella tertiolecta and its salt-sensitive mutant (HL 25/8). Plant Physiol. Biochem., 45(9):696-704.

[14]Goyal, A., 2007b. Osmoregulation in Dunaliella, Part II: photosynthesis and starch contribute carbon for glycerol synthesis during a salt stress in Dunaliella tertiolecta. Plant Physiol. Biochem., 45(9):705-710.

[15]Grabherr, M.G., Haas, B.J., Yassour, M., et al., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29(7):644-654.

[16]Hamana, K., Matsuzaki, S., 1982. Widespread occurrence of norspermidine and norspermine in eukaryotic algae. J. Biochem., 91(4):1321-1328.

[17]Huson, D.H., Mitra, S., Ruscheweyh, H.J., et al., 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Res., 21(9):1552-1560.

[18]Jensen, L.J., Julien, P., Kuhn, M., et al., 2008. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res., 36(Databse issue):D250-D254.

[19]Kim, J., Smith, J.J., Tian, L., et al., 2009. The evolution and function of carotenoid hydroxylases in Arabidopsis. Plant Cell Physiol., 50(3):463-479.

[20]Liu, H., Wu, W., Hou, K., et al., 2015. Transcriptome changes in Polygonum multiflorum Thunb. roots induced by methyl jasmonate. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 16(12):1027-1041.

[21]Liu, J., Zhang, D., Hong, L., 2014. Isolation, characterization and functional annotation of the salt tolerance genes through screening the high-quality cDNA library of the halophytic green alga Dunaliella salina (Chlorophyta). Ann. Microbiol., 24(3):1293-1302.

[22]Marco, F., Alcázar, R.N., Tiburcio, A.F., et al., 2011. Interactions between polyamines and abiotic stress pathway responses unraveled by transcriptome analysis of polyamine overproducers. OMICS, 15(11):775-782.

[23]Mishra, A., Mandoli, A., Jha, B., 2008. Physiological characterization and stress-induced metabolic responses of Dunaliella salina isolated from salt pan. J. Ind. Microbiol. Biot., 35(10):1093-1101.

[24]Mogedas, B., Casal, C., Forján, E., et al., 2009. β-Carotene production enhancement by UV-A radiation in Dunaliella bardawil cultivated in laboratory reactors. J. Biosci. Bioeng., 108(1):47-51.

[25]Moriya, Y., Itoh, M., Okuda, S., et al., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res., 35(Suppl. 2):W182-W185.

[26]Mortazavi, A., Williams, B.A., McCue, K., et al., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5(7):621-628.

[27]Rabbani, S., Beyer, P., Lintig, J.V., et al., 1998. Induced β-carotene synthesis driven by triacylglycerol deposition in the unicellular alga Dunaliella bardawil. Plant Physiol., 116:1239-1248.

[28]Rad, F.A., Aksoz, N., Hejazi, M.A., 2011. Effect of salinity on cell growth and β-carotene production in Dunaliella sp. isolates from Urmia Lake in northwest of Ira. Afr. J. Biotechnol., 10(12):2282-2289.

[29]Ramos, A.A., Polle, J., Tran, D., et al., 2011. The unicellular green alga Dunaliella salina Teod. as a model for abiotic stress tolerance: genetic advances and future perspectives. Harmful Algae, 26(1):3-20.

[30]Rismani-Yazdi, H., Haznedaroglu, B.Z., Bibby, K., et al., 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.

[31]Sathasivam, R., Kermanee, P., Roytrakul, S., et al., 2012. Isolation and molecular identification of β-carotene producing strains of Dunaliella salina and Dunaliella bardawil from salt soil samples by using species-specific primers and internal transcribed spacer (ITS) primers. Afr. J. Biotechnol., 11(102):16677-16687.

[32]Smith, D.R., Lee, R.W., Cushman, J.C., et al., 2010. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biol., 10:14.

[33]Steinbrenner, J., Linden, H., 2001. Regulation of two carotenoid biosynthesis genes coding for phytoene synthase and carotenoid hydroxylase during stress-induced astaxanthin formation in the green alga Haematococcus pluvialis. Plant Physiol., 125(2):810-817.

[34]Surget-Groba, Y., Montoya-Burgos, J.I., 2010. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res., 20:1432-1440.

[35]Theiss, C., Bohley, P., Voigt, J., 2002. Regulation by polyamines of ornithine decarboxylase activity and cell division in the unicellular green alga Chlamydomonas reinhardtii. Plant Physiol., 128(4):1470-1479.

[36]Tian, J., Yu, J., 2009. Changes in ultrastructure and responses of antioxidant systems of algae (Dunaliella salina) during acclimation to enhanced ultraviolet-B radiation. J. Photochem. Photobiol. B, 97(3):152-160.

[37]Tran, D., Haven, J., Qiu, W.G., et al., 2009. An update on carotenoid biosynthesis in algae: phylogenetic evidence for the existence of two classes of phytoene synthase. Planta, 229(3):723-729.

[38]Varela, J.C., Pereira, H., Vila, M., et al., 2015. Production of carotenoids by microalgae: achievements and challenges. Photosynth. Res., 125:423-436.

[39]Venekamp, J.H., 2006. Regulation of cytosol acidity in plants under conditions of drought. Physiol. Plantarum, 76(1):112-117.

[40]Voigt, J., Deinert, B., Bohley, P., 2000. Subcellular localization and light-dark control of ornithine decarboxylase in the unicellular green alga Chlamydomonas reinhardtii. Physiol. Plant, 108(2000):353-360.

[41]Wang, X., Xia, X., Huang, F., et al., 2012. Genetic modification of secondary metabolite biosynthesis in higher plants: a review. J. Biotechnol., 28(10):1151-1163 (in Chinese).

[42]Wang, Z., Fang, B., Chen, J., et al., 2010. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics, 11: 726-739.

[43]Xu, D.L., Long, H., Liang, J.J., et al., 2012. De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics, 13:133-141.

[44]Zhao, R., Cao, Y., Xu, H., et al., 2011. Analysis of espressed sequence tags from the green alga Dunaliella salina (Chalrophyta). J. Phycol., 47(6):1454-1460.

[45]List of electronic supplementary materials

[46]Data S1 Sequences of the genes identified in D. salina transcriptome

[47]Table S1 Primers of those selective genes involved in the metabolic processes in D. salina

[48]Table S2 Summary of annotation of D. salina transcriptome

[49]Table S3 Top-hit species (viridiplantae) list of D. salina BLAST-annotated uniseqs

[50]Table S4 Enzymes identified in metabolism of osmolytes (glycerol and proline), polyamines, and carotenoid through annotation of D. salina transcriptome

[51]Table S5 The best hit of the highlighted enzymes in the metabolic processes of D. salina

[52]Fig. S1 KOG (euKaryotic Ortholog Groups) functional classification of D. salina uniseqs

[53]Fig. S2 Gene ontology (GO) annotation of D. salina transcriptome

[54]Fig. S3 KEGG functional analyses of D. salina uniseqs

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