Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis
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 char...
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PeerJ Inc.
2017-11-01
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| author | Han Ming Gan Bolaji N. Thomas Nicole T. Cavanaugh Grace H. Morales Ashley N. Mayers Michael A. Savka André O. Hudson |
| author_facet | Han Ming Gan Bolaji N. Thomas Nicole T. Cavanaugh Grace H. Morales Ashley N. Mayers Michael A. Savka André O. Hudson |
| author_sort | Han Ming Gan |
| collection | DOAJ |
| description | 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. |
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| language | English |
| last_indexed | 2024-03-09T05:15:04Z |
| publishDate | 2017-11-01 |
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| spelling | doaj.art-8ebf5b7ff7b04de887512665a83e95442023-12-03T12:46:30ZengPeerJ Inc.PeerJ2167-83592017-11-015e403010.7717/peerj.4030Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesisHan Ming Gan0Bolaji N. Thomas1Nicole T. Cavanaugh2Grace H. Morales3Ashley N. Mayers4Michael A. Savka5André O. Hudson6Centre for Integrative Ecology-School of Life and Environmental Sciences, Deakin University, Victoria, AustraliaCollege of Health Science and Technology, Rochester Institute of Technology, Rochester, NY, United States of AmericaThomas H. Gosnell School of School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USAThomas H. Gosnell School of School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USACollege of Health Science and Technology, Rochester Institute of Technology, Rochester, NY, United States of AmericaThomas H. Gosnell School of School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USAThomas H. Gosnell School of School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USAIn 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.https://peerj.com/articles/4030.pdfRhodotorula mucilaginosaCarotenoidPhylogenomicsEndophyteNext-generation sequencingChew sticks mitogenome |
| spellingShingle | Han Ming Gan Bolaji N. Thomas Nicole T. Cavanaugh Grace H. Morales Ashley N. Mayers Michael A. Savka André O. Hudson Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis PeerJ Rhodotorula mucilaginosa Carotenoid Phylogenomics Endophyte Next-generation sequencing Chew sticks mitogenome |
| title | Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis |
| title_full | Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis |
| title_fullStr | Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis |
| title_full_unstemmed | Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis |
| title_short | Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis |
| title_sort | whole genome sequencing of rhodotorula mucilaginosa isolated from the chewing stick distemonanthus benthamianus insights into rhodotorula phylogeny mitogenome dynamics and carotenoid biosynthesis |
| topic | Rhodotorula mucilaginosa Carotenoid Phylogenomics Endophyte Next-generation sequencing Chew sticks mitogenome |
| url | https://peerj.com/articles/4030.pdf |
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