Rhodotorula species are ubiquitous saprophytic yeasts that can be recovered from many environmental. Here we present the genome sequence of rhodotorula graminis wp1, a pinkpigmented, encapsulated yeast strain belonging to the basidiomycota phylum that was isolated from within stems of populus trichocarpa growing in its native riparian environment alongside the snoqualmie river in western washington statexin et al. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091. High rhodotorula sequences in skin transcriptome of patients. Engineering an efficient and tight damino acidinducible gene expression system in rhodosporidium. A molecular approach was applied to the study of the carotenoid biosynthetic pathway of rhodotorula mucilaginosa.
The genus microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Strain wp1 was isolated as an endophyte along with an assortment of bacteria within populus trichocarpa black cottonwood. Rhodotorula kratochvilovae strain ls11 is a biocontrol agent bca selected for its antagonistic activity against several plant. Component name genome accessions component representation.
Comparative analysis of protein families and genes. Genome sequence of the oleaginous yeast rhodotorula glutinis. However, there is little information about genome sequence of acidictolerant rhodotorula strain with phenoldegrading. Previous studies have suggested a role for pathogens as a trigger of systemic sclerosis ssc, although neither a pathogen nor a mechanism of pathogenesis is known. Rhodotorula mucilaginosa jgtas1 genome sequencing project has been deposited in ncbi under bioproject prjna393004 and biosample. Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, rhodotorula rhodosporidium toruloides pucciniomycotina is known to produce high quantities of lipids when grown in nitrogenlimiting media, and has potential for biodiesel production. Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. Comparative genome analysis of the oleaginous yeast trichosporon. Genomewide identification and evaluation of constitutive promoters in streptomycetes. Little is known about the metabolic aspects of lipid production from the lignocellolosic sugar xylose by oleaginous yeasts in general and r. Proteome analysis of xylose metabolism in rhodotorula.
Mitochondrial genome was assembled separately and is available in the downloads section. Then, a set of genes involved in different steps of carotenogenesis was identified and those coding for phytoene desaturase. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091 article pdf available in genome announcements 21 january 2014 with 3 reads how we measure reads. Wholegenome sequencing of an acidophilic rhodotorula sp. The upstream dna sequences of 6 genes involved in lipid biosynthesis or. Engineering an efficient and tight d amino acidinducible. Engineering an efficient and tight damino acidinducible. Harrison, transactions of the royal society of canada.
Molecular phylogenetics of the genus rhodotorula and related. Rhodotorula species are pigmented basidiomycetous yeasts in the family sporidiobolaceae 21. It is one of the few species of the genus candida which cause candidiasis in humans. The ngr genome has predicted 5963 proteincoding genes, and the most of genes were annotated into the specie r. Lifestyle, citing the centers for disease control and prevention. Candida auris is a species of fungus that grows as yeast. Draft genome sequence of rhodotorula mucilaginosa, an emergent. Engineering the oleaginous red yeast rhodotorula glutinis for. Aevr00000000 rhodotorula toruloides atcc 204091, whole genome shotgun sequencing project references pathak r, yadav nk. High rhodotorula sequences in skin transcriptome of.
Pal phenylalanine ammonia lyase rhodotorula glutinis. The results demonstrated that the basidiomycetous yeasts under investigation distributed into two main clusters. Genetic analysis of dxylose metabolism by endophytic. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091 article pdf available january 2014 with 99 reads how we measure reads. We have adapted agrobacterium tumefaciensmediated transformation atmt as a genetagging tool for the identification of novel genes in r. Whole genome sequencing and comparative genomic analysis of.
Rhodotorula rhodosporidium toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to i enhance its natural production of lipids and carotenoids, and ii produce novel industrially relevant compounds. Molecular phylogenetics of the genus rhodotorula and. The fungus is a common colonist of animals, foods and environmental materials. Lipids accumulation in rhodotorula glutinis and cryptococcus. Introduction rhodotorula and rhodosporidium produce the major carotenoid pigments, carotene, torulene and torularhodin. Developing a set of strong intronic promoters for robust. Developing a set of strong intronic promoters for robust metabolic engineering in oleaginous rhodotorula rhodosporidium yeast species. Rhodotorula mucilaginosa assembly asm280678v1 download sequences in fasta format for genome. Harrison is a pink glistening pucciniomycotina basidiomycota yeast species that is commonly isolated from air, freshwater and seawater all over the world. Identification of different species of rhodotorula using. In present, there are studies describing the genome sequence of r.
This study presents the first proteome analysis of the metabolism of r. Phylogenetic relationships of basidiomycetous yeasts, especially of the genus rhodotorula, were studied using partial sequences of the mitochondrial cytochrome b gene. Genome sequence of the plant growth promoting endophytic yeast rhodotorula graminis wp1. Rhodosporidium toruloides strain atcc 204091 iip 30. Rhodotorula glutinis is an oleaginous oxidative red yeast that potentially can be used for biodiesel production as well as other important products, such as carotenoids torulene, torularhodin. Three novel species, which are nonpathogenic to humans, have. The strain selected for genome sequencing was isolated from the mycangia of sirex wasp in louisiana, usa.
Fatty acids represent important substrates for obtaining microbial lipases and biosurfactants. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc. This is an updated paper focusing on the general epidemiological aspects of rhodotorula in humans, animals, and the environment. Further, we report for the first time, the recovery of the complete mitochondrial genome of r. Car gene cluster and transcript levels of carotenogenic. Influence of cultural conditions on lipid production by mutant strain of rhodotorula glutinis mtcc 1151. Price was able to assemble additional contigs whose best alignment was to rhodotorula genes, though the longest contig in each sample was a sequence whose best alignment in the nt database was to r. Arturo casadevall, md, phd, and molecular microbiology and immunology chair at. Fast and efficient genetic transformation of oleaginous yeast. Aligning raw reads to rhodotorula glutinis 28s rrna sequence fj345357 shows many reads aligning in the systemic sclerosis ssc samples but much fewer reads in the normal samples. Genome wide identification and evaluation of constitutive promoters in streptomycetes.
Multiple sequence alignment is discussed in light of homology. Fatty acids effect on lipase and biosurfactant induction in. Microbotryum lychnidisdioicae infects silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Rhodotorula toruloides is a promising platform organism for production of lipids from lignocellulosic substrates. Rnaseq was performed on four ssc patients and four controls, to a depth of 200 million reads. Therefore, it is vital to sequence the wholegenome rhodotorula sp. Rhodotorula mucilaginosa is a common saprophytic fungus that is a part of the basidiomycota phylum. Till now, two rhodotorula dao1 sequences have been deposited with genbank accession numbers. Draft genome sequences of both strains are reported here.
Species of rhodotorula were distributed in all of these clades, indicating the polyphyletic nature of the genus. Fatty acids effect on lipase and biosurfactant induction. Publications genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091. Red yeast species in the rhodotorularhodosporidium genus are outstanding. The putative homolog of acc1, acl1, fas1, fat1, dur1 and ldp1 was found located in the genome sequencing scaffold no. Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels.
Rhodotorula graminis wp1 was found to endophytically colonize poplar. The genus contains 37 species, of which only three, including r. Genome sequence of the plant growth promoting endophytic. Genome sequence of the plant growth promoting endophytic yeast rhodotorula graminis wp1 andrea firrincieli, 1 robert otillar, 2 asaf salamov, 2 jeremy schmutz, 2, 3 zareen khan, 4 regina s. Mattheos koffass lab contains the insert rgtalsyn and is published in mbio. Microorganisms free fulltext rhodotorula mucilaginosa. Pdf genome sequence of the oleaginous yeast rhodotorula. In order to exclude the inherent quality of yeast, we added the model yeast s. The engineering potential of rhodosporidium toruloides as. We have developed a luciferase gene reporter assay based on a new codonoptimized luc2 reporter gene rtluc2, which is flanked with car2 homology arms and can be integrated. Currently, information on the key metabolic pathways and their molecular basis of regulation remains scarce, severely limiting efforts to engineer it as an industrial host. Rhodotorula mucilaginosa jgtas1 genome sequencing project has been deposited in ncbi under. Oct 26, 2015 rhodosporidium and rhodotorula are two genera of oleaginous red yeast with great potential for industrial biotechnology. Genome annotation predicts 7,642 proteinencoding genes.
Strain wp1 was isolated as an endophyte along with an assortment of bacteria within populus trichocarpa black cottonwood growing. Systems used to automatically annotate proteins with high accuracy. The current assembly of strain atcc 10788 comprises 61 scaffolds with a total size of 20. Here we show enrichment of rhodotorula sequences in the skin of patients with early, diffuse ssc compared with that in normal controls. Bioremediation is an ecological modern technology of great interest for. June 2016 the rhodotorula glutinis atcc 28052 genome was sequenced with illumina, assembled with allpathslg, and annotated with the jgi annotation pipeline. Engineering corynebacterium glutamicum for the production of 2,3butanediol engineering corynebacterium glutamicum for the production of 2,3butanediol. 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. The position shown is from 750 to 1,100 in the sequence, which is the end of its2, and the first 400 bases of 28s rrna. Genome wide identification and evaluation of constitutive promoters in.
Heterogeneity of the genus has made its classification difficult with five varieties having been recognized. Race and transcriptomics showed that the cdna of acc1, acl1, fas1, fat1, dur1 and ldp1 contains a 5. Crossref carlos rolz, two consecutive step process for ethanol and microbial oil production from sweet sorghum juice, biochemical engineering journal, 112, 186, 2016. Rhodosporidium toruloides atcc 10788 haploid, a1 mating type and atcc 10657 haploid, a2 mating type were derived from the same diploid parent strain rhodotorula glutinis atcc 90781 and are important strains for metabolic engineering. The yeast strain cmgbrg5 was identified as rhodotorula glutinis using the biolog microlog system. Rhodosporidium glutinis atcc 204091 also known as rhodosporidium toruloides is a pinkcolored oleaginous fungus.
Rhodotorula glutinis, rhodotorula minuta and rhodotorula mucilaginosa formerly known as. Cbs 20, ccrc 21418, ifo 1125, mucl 30253, nrrl y2502, ucd 68255, vkm y332 application. Of the numerous species in the genus rhodotorula,onlyrhodotorula mucilaginosa,rhodotorula glutinis, andrhodotorula minuta. 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. Whole genome sequencing and comparative genomic analysis. Genome sequence of the oleaginous yeast rhodotorula.
Therefore, it is vital to sequence the whole genome rhodotorula sp. This motivates us to perform a comparative genomic analysis between s. Often, candidiasis is acquired in hospitals by patients with weakened immune systems. Given that rrna is present at much higher quantities than other transcripts, this is not unsurprising. Whole genome sequencing of rhodotorula mucilaginosa. The engineering potential of rhodosporidium toruloides as a. Compared to the lacking ballistospores rhodotorula toruloides and saccharomyces.
Genetic transformation of the yeast rhodotorula gracilis. This is the first report describing the cloning and characterization of the. Although xr and xdh activities were detected in rhodosporidium toruloides the teleomorph of rhodotorula glutinis freer et al. Sep 17, 2015 background here we present the genome sequence of rhodotorula graminis wp1, a pinkpigmented, encapsulated yeast strain belonging to the basidiomycota phylum and isolated from within stems of populus trichocarpa growing in its native riparian environment alongside the snoqualmie river in western washington state xin et al.
Frontiers genome sequence of the plant growth promoting. Rhodosporidium toruloides strain atcc 204091 iip 30 mtcc. Rhodotorula glutinis an overview sciencedirect topics. Rhodotorula mucilaginosa, a yeast with valuable biotechnological features, has also been recorded as an emergent opportunistic. Previously considered nonpathogenic, rhodotorula species have emerged as opportunistic pathogens that have the ability to colonise and infect susceptible patients.
Fast and efficient genetic transformation of oleaginous. Whole genome sequencing of rhodotorula mucilaginosa isolated. At first, functional annotation of the genome of r. This species has also been implicated in rare human infections. Rhodotorula kratochvilovae strain ls11 is a biocontrol agent bca selected for its antagonistic activity against several plant pathogens both in the field and postharvest. A limited number of rhodotorula species demonstrated identical sequences, for example rhodotorula bacarum and rhodotorula foliorum, rhodotorula fujisanensis and rhodotorula futronensis, rhodotorula glutinis var.
Car gene cluster and transcript levels of carotenogenic genes. Microorganisms free fulltext rhodotorula mucilaginosa c2. Genome assembly includes 62 contigs for a total of 22. Unirule expertly curated rules saas system generated rules. Complete genome sequence of the biocontrol agent yeast. Help pages, faqs, uniprotkb manual, documents, news archive and biocuration projects. However, the type, concentration and yield of various carotenoids are depending on. Integrative genomics viewer igv visualization of original read set to r. Paul d, magbanua z, ma ii, french t, bridges sm, burgess sc, et al. Rhodotorula species have been isolated from a wide variety of environmental sources as diverse as active deep sea volcanoes and wastewater treatment areas and are associated with a range of plant species. It was isolated from soil in baroda, india and can grow on a wide range of carbon sources. Draft genome sequences of rhodosporidium toruloides. Identification of different species of rhodotorula using internal transcribed spacers mona abd elmageed mohamed, asharf bakery abdelrazik and samir abdelaziz. The rhodosporidium glutinis atcc 204091 was not sequenced or assembled at the doe joint genome institute.662 1603 1102 705 1043 330 1213 260 1415 834 730 1206 1021 420 999 1563 1463 309 976 549 125 1185 836 877 92 352 152 819 403 441 1126