Analysis of the Transcriptome of Dunaliella Sp. (Chlorophyta) by cDNA Microarray

Abstract

Analysis of the transcriptome of Dunaliella sp. (chlorophyta) by cDNA microaray

MinJung Kim, SeunHye Park, Myung-Soo Han and EonSeon Jin* Department of Life Science, College of Natural Science, Hanyang University, 133-791 Seoul, South Korea

Algae of the genus Dunaliella are known to grow in a wide range of salinities. To investigate which genes may be important for growth under extremely low or high salinities, a survey of the Dunaliella sp. transcriptome was performed by microarray analysis. For the cDNA microarray, 778 expressed sequence tags (ESTs) were generated from a cDNA library of Dunaliella sp. in our previous study. The cDNA microarray was used to compare the transcription profiles of cells acclimated to extreme saline conditions (0.08 M NaCl and 4.5 M NaCl) with the transcription profile of cells acclimated to an intermediate salinity (1.5 M NaCl). The comparative microarray analysis indicated that 183 out of the 778 ESTs differed in expression levels by more than two-fold in cells grown at extreme salinities when compared to cells grown at intermediate salinity (1.5M NaCl). The sequences of these 183 cDNAs were classified into 142 non-redundant gene clusters. Of these genes, 28 had increased expression and 57 were suppressed in cells grown at low salinity. In cells grown at high salinity, 43 genes showed increased expression and 69 genes showed suppressed expression. One hundred twelve genes were up- or down-regulated by high salinity (4.5M NaCl). Of the high salinity-regulated genes, 49% were also influenced by low salinity (0.08M NaCl), revealing a dense overlap of genes involved in low and high salt responses. Only 30 genes were independently regulated in the low salt condition. However, we did observe a large overlap in the expression of extreme salinity-responsive genes based on Venn diagram analysis, which found 55 genes that responded to both of the two extreme salinity conditions. The results of our refined expression analysis using gene-specific primers and real-time PCR for selected transcripts was in agreement with the microarray results for most genes tested. This study is the first large-scale survey of the transcriptome from the microalga Dunaliella sp. and provides a platform for further functional investigation of differentially expressed genes in Dunaliella.