Comparative Genomic Analysis of the Mutant Rhodotorula mucilaginosa JH-R23 Provides Insight into the High-Yield Carotenoid Mechanism

In this study, the wild-type Rhodotorula mucilaginosa GDMCC 2.30 and its high carotenoid-producing mutant JH-R23, which was screened from the space mutation breeding treated wild type, were used as materials. Through whole-genome sequencing and resequencing analysis, the carotenoid metabolic pathway and mechanism of high carotenoid production in the mutant were explored. The R. mucilaginosa GDMCC 2.30 genome comprised 18 scaffolds and one circular mitochondrial genome with a total size of 20.31 Mb, a GC content of 60.52%, and encoding 7128 genes. The mitochondrial genome comprised 40,152 bp with a GC content of 40.59%. Based on functional annotations in the GO, KEGG, and other protein databases, nine candidate genes associated with carotenoid metabolic pathways, and candidate genes of the CrtS and CrtR homologous gene families were identified. The carotenoid metabolic pathway was inferred to start from sugar metabolism to the mevalonate pathway, as is common to most fungi, and the final product of the mevalonate pathway, geranylgeranyl diphosphate, is a precursor for various carotenoids, including β-carotene, lycopene, astaxanthin, and torularhodin, formed through the activity of crucial enzymes encoded by genes such as CrtI, CrtYB, CrtS, and CrtR. Resequencing analysis of the mutant JH-R23 detected mutations in the exons of four genes, including those encoding Gal83, 3-oxoacyl-reductase, p24 proteins, and GTPase. These mutations are interpreted to have an important impact on carotenoid synthesis by JH-R23.