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Background  The biomass yield of  Chlorella  PY-ZU1 drastically increased when cultivated under high CO 2  condition compared with that cultivated under air condition. However, less attention has been given to the microalgae photosynthetic mechanisms response to different CO 2  concentrations. The genetic reasons for the higher growth rate, CO 2  fixation rate, and photosynthetic efficiency of microalgal cells under higher CO 2  concentration have not been clearly defined yet.    Results  In this study, the Illumina sequencing and de novo transcriptome assembly of  Chlorella  PY-ZU1 cells cultivated under 15% CO 2  were performed and compared with those of cells grown under air. It was found that carbonic anhydrase (CAs, enzyme for interconversion of bicarbonate to CO 2 ) dramatically decreased to near 0 in 15% CO 2 -grown cells, which indicated that CO 2  molecules directly permeated into cells under high CO 2  stress without CO 2 -concentrating mechanism. Extrapolating from the growth conditions and quantitative Real-Time PCR of CCM-related genes, the  K   m  (CO 2 ) (the minimum intracellular CO 2  concentration that rubisco required) of  Chlorella  PY-ZU1 might be in the range of 80–192 μM. More adenosine triphosphates was saved for carbon fixation-related pathways. The transcript abundance of rubisco (the most important enzyme of CO 2  fixation reaction) was 16.3 times higher in 15% CO 2 -grown cells than that under air. Besides, the transcript abundances of most key genes involved in carbon fixation pathways were also enhanced in 15% CO 2 -grown cells.    Conclusions  Carbon fixation and nitrogen metabolism are the two most important metabolisms in the photosynthetic cells. These genes related to the two most metabolisms with significantly differential expressions were beneficial for microalgal growth (2.85 g L −1 ) under 15% CO 2  concentration. Considering the micro and macro growth phenomena of  Chlorella  PY-ZU1 under different concentrations of CO 2  (0.04–60%), CO 2  transport pathways responses to different CO 2  (0.04–60%) concentrations was reconstructed.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-017-0868-z) contains supplementary material, which is available to authorized users.

Transcriptome and key genes expression related to carbon fixation pathways in Chlorella PY-ZU1 cells and their growth under high concentrations of CO2