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

Han Ming Gan,Nicole T Cavanaugh,André O Hudson,Michael A Savka,Grace H Morales,Bolaji N Thomas,Ashley N Mayers

doi:10.7717/peerj.4030

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.

Highlights

Rhodotorula mucilaginosa is a common saprophytic fungus that is a part of the Basidiomycota phylum
GenomeScope estimated a genome size of 18.6 mega base pairs (Mbp) with an estimated heterozygosity of 9.29% for strain RIT389 (Fig. 2)
De novo assembly using sub-sampled reads enabled the recovery of the complete mitogenome of strain RIT389 which is the first mitogenome reported for this genus

Summary

Introduction

Rhodotorula mucilaginosa is a common saprophytic fungus that is a part of the Basidiomycota phylum. Of the numerous species in the genus Rhodotorula, only Rhodotorula mucilaginosa, Rhodotorula glutinis, and Rhodotorula minuta have been known to be pathogenic to humans (Wirth & Goldani, 2012; Zaas et al, 2003). Despite being categorized as an opportunistic and emerging pathogen, R. mucilaginosa from natural environments appear to possess interesting biological traits ranging from indole acetic acid production (plant growth-promoting), bacterial quorum sensing signal degradation (quorum quenching) to carotenoid production (Ghani et al, 2014; Ignatova et al, 2015; Libkind, Brizzio & Broock, 2004). Resources for R. mucilaginosa are surprisingly scarce in public database. The only genomic resource publicly available for this species is from R. mucilaginosa strain C2.5t1 that was isolated from the seeds of the cacao plant in Cameroon (Deligios et al, 2015). Beyond the NCBI database, another genome of R. mulaginosa (strain ATCC58901) can be found in the JGI portal (https://genome.jgi.doe.gov/Rhomuc1/Rhomuc1.home.html) but a user account is required to access the genome

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Conclusion