De novo transcriptomic and metabolomic analysis of docosahexaenoic acid (DHA)-producing Crypthecodinium cohnii during fed-batch fermentation

The heterotrophic microalga Crypthecodinium cohnii accumulates lipids with a high fraction of docosahexaenoic acid (DHA). However, lack of genomic information limits the understanding of its physiological metabolism for better DHA production. In this study, de novo assembly of the C. cohnii transcriptome from three growth stages (i.e., fast growth, fatty acid accumulation and DHA conversion stages) was conducted, leading to identification of a total of 82,106 unigenes with an N50 of 1822 bp, among which 64.7% were annotated based on sequence similarity to known genes in the database. In addition, pathway enrichment analysis showed that transcripts related to fatty acid biosynthesis, starch and sucrose metabolism as well as biosynthesis of unsaturated fatty acids were significantly up-regulated during late-stage fermentation. Interestingly, several polyketide synthases (PKSs) and multiple fatty acid desaturases potentially involved in DHA biosynthesis were identified in the C. cohnii transcriptome, most of which were significantly up-regulated during lipid and DHA accumulation, implying that C. cohnii might utilize a combination of PKS systems and desaturase steps for DHA biosynthesis. The results were further confirmed by qRT-PCR and GC-MS-based metabolomic analyses. Overall, integrative analysis of de novo transcriptomic and metabolomic data provided important functional genomic information necessary for not only a better understanding of C. cohnii growth and DHA biosynthesis but also future genetic engineering of industry-important C. cohnii.