Insights into genomics and gene expression of oleaginous yeasts of the genus Rhodoturula

Abstract

The Rhodotorula glutinis cluster includes oleaginous yeast species with high biotechnological potential as cell factories for lipid, carotenoid, and oleochemical production. They can grow on various low-cost residues, such as lignocellulose and crude glycerol. The accumulated microbial lipids have a fatty acid composition similar to vegetable oils, representing a sustainable alternative in food, feed, and biofuel industries. Strain manipulation could further increase its economic attractiveness. A basic prerequisite for this is to understand the genome organization of Rhodotorula spp. and the lipid and carotenoid metabolism on residual products in detail. This doctoral thesis made a substantial contribution to this: Hybrid genome assemblies from R. toruloides, R. glutinis, and R. babjevae were built de novo using a combination of short- and long-read sequencing. By doing this, high-quality genomes could be achieved, showing high completeness and contiguity (near-chromosome level). Among other things, this enabled the prediction of ploidy and the discovery of extrachromosomal structures. Phylogenetic analyses revealed high intraspecific divergence in R. babjevae. Using RNA-seq data generated from different growth conditions, gene annotation for R. toruloides could be significantly increased, and comprehensive gene expression data could be obtained. These allowed conclusions to be drawn about the activation and mechanism of lipid accumulation in R. toruloides grown on residual products such as crude glycerol and hemicellulosic hydrolysate.