Strain-specific diversity in lipid and carotenoid profiles of Rhodotorula toruloides

Rhodotorula toruloides is known for its capacity to produce lipids and carotenoids with potential biotechnological applications. In this study, we investigated strain-specific differences in lipid and carotenoid production among R. toruloides CBS 14, CBS 349, and the type-strain CBS 6016 ^T , a hybrid of the former two, alongside with a comparative genomic approach. Four main carotenoids were identified in all three strains: β-carotene, γ-carotene, torularhodin and torulene, with torularhodin being the most abundant. CBS 14 and CBS 6016 ^T displayed similar metabolic profiles, with total carotenoid levels of 58.04 ± 0.35 and 44.52 ± 1.75 μg/g (cell dry weight), and lipid concentrations of 6.48 ± 0.04 and 7.46 ± 0.5 g/L, respectively. In contrast, CBS 349 produced significantly less carotenoids (4.85 ± 0.03 μg/g) and lipids (2.17 ± 0.31 g/L). Oleic acid was the dominant fatty acid in all strains, followed by palmitic and linoleic acids. Genomic analysis showed that CBS 14 and CBS 6016 share conserved genetic features related to lipid and carotenoid metabolism, whereas CBS 349 harbors truncated or fragmented key genes such as FAS1 , AL2 , and ACACA , consistent with its observed impaired lipid and carotenoid production. FAA homologs in CBS 349 were partly truncated, likely impairing fatty acid utilization. The hybrid CBS 6016 ^T carried double sets of genes equally originated from both parental strains, but increased gene number did not translate into higher lipid production.