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In industry, the yeast  Rhodotorula mucilaginosa  is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus  Rhodotorula  is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte  R. mucilaginosa  RIT389 isolated from  Distemonanthus benthamianus,  a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of  R. mucilaginosa  RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced  Rhodotorula  species. Further, we report for the first time, the recovery of the complete mitochondrial genome of  R. mucilaginosa  using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of  Rhodotorula taiwanensis  which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in  R. mucilaginosa  RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

peerj

Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis