RNA-seq of Chlorella sp. HS2: Comparison between freshwater and marine conditions at exponential and stationary growth phases

Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained. Algal cultures grown in marine medium (3% (w/v) of supplemental sea salt) was compared to the cultures grown in freshwater medium, at the exponential growth phase (4 days after the beginning of the cultivation) and then at the stationary growth phase (6 days). Each condition had 3 biological replicates, resulting in the total of 12 samples. Samples were sequenced by 100 bp paired-end Illumina HiSeq 2000 platform. We processed raw reads using Trinity for de novo assembly and RSEM for count quantification, to perform differential expression analysis of genes with SVCD for the count normalization and DESeq2 for the statistical test. Gene isoforms were annotated by the Trinotate pipeline (BlastX, TransDecoder and BlastP)