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

Abstract

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.

Torulene and torularhodin: “new” fungal carotenoids for industry?

“…In recent years, the use of molecular and -omics tools in the characterization of red yeast has increased [ 55 ]. To date, whole genome sequences of some carotenogenic yeast have been identified, for example R. glutinis ATCC 204091 [ 56 ], R. graminis WP1 [ 57 ], R. mucilaginosa RIT389 [ 58 ] R. toruloides ATCC 10788 and ATCC 10657 [ 59 ], R. toruloides MTCC 457 [ 60 ], R. toruloides CECT1137 [ 61 ], and R. toruloides CGMCC 2.1609 [ 62 ]. Genome sequencing of R. toruloides NP11 has led to the identification of two genes that code carotenoid synthesis-related enzymes, phytoene synthase ( PSY1 ) and phytoene dehydrogenase ( CRTI ) [ 63 ].…”

“…Genome sequencing of R. toruloides NP11 has led to the identification of two genes that code carotenoid synthesis-related enzymes, phytoene synthase ( PSY1 ) and phytoene dehydrogenase ( CRTI ) [ 63 ]. Gan et al [ 58 ] identified genomic regions containing the key genes for carotenoid production in R. mucilaginosa . The genes coding for phytoene synthase ( crtB ), lycopene cyclase ( crtY ), and phytoene desaturase ( crtI ) were located in relatively close proximity to one another.…”

Biosynthetic Pathway of Carotenoids in Rhodotorula and Strategies for Enhanced Their Production

“…The whole genome of R. mucilaginosa RIT389 was sequenced with the identification of a genomic region associated with carotenoid, in which three genes encoding phytoene synthase (crtB), lycopene cyclase (crtY), and phytoene desaturase (crtI) were found closely located, whereas the gene encoding geranyl pyrophosphate synthase was located apart at a separate contig. The two other key genes, crtX and crtBY, that encoded carotenoid oxygenase and phytoene synthase/ lycopene cyclase, respectively, were found located in close proximity and convergently transcribed in all the species in Rhodotorula (except for R. mucilaginosa) [60]. On the base of the genome sequence of R. mucilaginosa C2.5t1, a set of genes involved in carotenogenesis were identified.…”

Characterization of the complete mitochondrial genome of biocontrol yeast Sporobolomyces sp. (Sporidiobolales: Sporidiobolaceae) with phylogenetic analysis

“…As shown in the phylogenetic tree (Figure 1), the mitochondrial genome of Sporobolomyces sp. exhibited a close relationship with that of Rhodotorula mucilaginosa (Gan et al 2017).…”