Abstract Chlorella zofingiensis has great potential for astaxanthin and fatty acid production. This study investigated the accumulation of astaxanthin and total fatty acids (TFA), the fatty acid compositions of astaxanthin esters and TFA in photoautotrophic and heterotrophic C. zofingiensis, respectively. The results displayed that in photoautotrophic cells, 18:3 was the most predominant fatty acid, followed by 16:0, 18:2, and 18:1, while astaxanthin mono‐esters (mono‐AE) contained only 16:0 and 18:0, and astaxanthin di‐esters (di‐AE) contained 16:0 mostly, followed by 18:1, 18:0, 18:2, and 18:3. C. zofingiensis accumulated the highest level of astaxanthin and TFA under heterotrophic conditions fed with 30 g L−1 glucose. The percentage of 18:1 in TFA, mono‐AE, and di‐AE increased from 10.05%, 0%, and 17.76% to 35.80%, 14.84%, and 50.12%, respectively; in contrast, the percentages of 18:3 in TFA and di‐AE were observed to decrease from 40.42% and 7.59% to 9.56% and 1.30%, respectively, in comparison with those in photoautotrophic ones. The RNA sequencing (RNA‐seq) results showed that the expressions of the genes in astaxanthin and fatty acid biosynthetic pathways were increased under this heterotrophic condition. These results indicated differential accumulation of AE and TFA, especially fatty acid compositions of TFA and AE in photoautotrophic and heterotrophic cells, suggesting a positive correlation between astaxanthin and fatty acid biosynthesis.
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