Gene expression profiling of Dunaliella sp. acclimated to different salinities Minjung Kim, 1 Seunghye Park, 1 Jürgen E.W. Polle 2 and EonSeon Jin 1 * 1 Department of Life Science, College of Natural Science, Hanyang University, 133-791 Seoul, Korea, and 2 Brooklyn College of the City University of New York, Biology Department, 2900 Bedford Ave, Brooklyn, New York 11210, USA SUMMARY To investigate which genes may be important for growth under extreme conditions such as very low or high salinities, a survey of the Dunaliella sp. transcriptome was performed with a cDNA microarray which had been generated previously representing 778 expressed sequence tags. The comparative microarray analysis indicated that 142 genes differed in expression levels by more than twofold in cells grown at extreme salinities (0.08 M and 4.5 M NaCl) when compared with cells grown at intermediate salinity (1.5 M NaCl). Of these genes, 28 had increased expression and 57 were sup- pressed in cells grown at low salinity. In cells grown at high salinity, 43 genes showed increased expression and 69 genes showed suppressed expression. However, we did observe a large overlap in the expression of extreme salinity-responsive genes based on Venn diagram analy- sis, which found 55 genes that responded to both of the two extreme salinity conditions. Further, we found that several genes had similar expression levels under low and high salinities, including some general stress response genes that were upregulated in both extreme salinity conditions. For confirmation of the validity of the cDNA microarray analysis, expression of several genes was independently confirmed by the use of gene-specific primers and real-time polymerase chain reaction. The present study is the first large-scale comparative survey of the transcriptome from the microalga Dunaliella sp. acclimated to extreme salinities, thus providing a plat- form for further functional investigation of differentially expressed genes in Dunaliella. Key words: cDNA microarray, Dunaliella sp., reverse transcription-polymerase chain reaction, salinity acclimation. INTRODUCTION The genus Dunaliella (Chlorophyta) contains unicellular species with ovoid biflagellate cells and cell volumes in the range of 100–1000 mm 3 (Avron & Ben-Amotz 1992). Species of the genus Dunaliella are known to grow optimally at salinities between 0.5 M to 2 M NaCl, under optimal growth conditions cells are green in color and contain only the pigments (carotenoids and chlorophyll) necessary for photosynthesis (McLachlan 1960; Borowitzka & Brown 1974). A number of the species from this genus are halotolerant, and some of these algae are model organisms for studies on accli- mation in response to changes in salinity. High salinity, high light, temperature changes, and drought are the most common environmental stress factors that influence the photoautotrophic growth of plants and algae (Rabbani et al. 2003). Among the different abiotic environmental stresses, external salin- ity can become a major stressor that inhibits cell pro- liferation and growth both in terrestrial and aquatic organisms. Salinity extremes will produce osmotic and/or ionic effects in photosynthetic organisms (Katz et al. 1992; Whiteley et al. 2001; Jahnke & White 2003). Salt stress responses are well studied at the molecular level in higher plants (Hasegawa et al. 2000; Kreps et al. 2002; Rabbani et al. 2003; Jiang et al. 2007). Recently, researchers developed an improved two-dimensional gel electrophoresis (2-DE) protocol (Liska et al. 2004) and introduced a proteomic approach for identifying salt-induced proteins from D. salina. Known salt stress-induced gene products com- prised transcripts and proteins involved in carbon and iron assimilation as well as carotenoid biosynthesis (Fisher et al. 1998; Coesel et al. 2008). Other than these studies there is only limited information about the molecular response to salinity stress in Dunaliella. cDNA microarray technology is revolutionizing many aspects of biological research by allowing simultaneous monitoring of the expression of several hundreds to thousands of gene transcripts in the context of complex biological processes (Schena et al. 1995; Shalon et al. 1996; Eom et al. 2006; Moseley et al. 2006). Microar- ray technology provides a relatively simple and economi- cal way to explore genome-wide changes in expression. *To whom correspondence should be addressed. Email: esjin@hanyang.ac.kr Communicating editor: J. M. Archibald. Received 20 December 2008; accepted 10 April 2009. doi: 10.1111/j.1440-1835.2009.00554.x Phycological Research 2010; 58: 17–28 © 2010 Japanese Society of Phycology