Rnaseq was performed on four ssc patients and four controls, to a depth of 200 million reads. Further, we report for the first time, the recovery of the complete mitochondrial genome of r. Rhodotorula kratochvilovae strain ls11 is a biocontrol agent bca selected for its antagonistic activity against several plant. Arturo casadevall, md, phd, and molecular microbiology and immunology chair at. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc. Car gene cluster and transcript levels of carotenogenic. Fatty acids represent important substrates for obtaining microbial lipases and biosurfactants. This study presents the first proteome analysis of the metabolism of r. 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. Although numerous bacterial endophytes, the microorganisms.
The putative homolog of acc1, acl1, fas1, fat1, dur1 and ldp1 was found located in the genome sequencing scaffold no. However, the type, concentration and yield of various carotenoids are depending on. However, there is little information about genome sequence of acidictolerant rhodotorula strain with phenoldegrading. Comparative genome analysis of the oleaginous yeast trichosporon. Genome sequence of the oleaginous yeast rhodotorula glutinis. We have adapted agrobacterium tumefaciensmediated transformation atmt as a genetagging tool for the identification of novel genes in r. Species of rhodotorula were distributed in all of these clades, indicating the polyphyletic nature of the genus. Multiple sequence alignment is discussed in light of homology.
Bioremediation is an ecological modern technology of great interest for. Red yeast species in the rhodotorularhodosporidium genus are outstanding. 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. 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 results demonstrated that the basidiomycetous yeasts under investigation distributed into two main clusters. Rhodotorula species are ubiquitous saprophytic yeasts that can be recovered from many environmental. Aevr00000000 rhodotorula toruloides atcc 204091, whole genome shotgun sequencing project references pathak r, yadav nk. Rhodotorula graminis wp1 was found to endophytically colonize poplar. Mattheos koffass lab contains the insert rgtalsyn and is published in mbio. This is the first report describing the cloning and characterization of the.
Genomewide identification and evaluation of constitutive promoters in streptomycetes. It was isolated from soil in baroda, india and can grow on a wide range of carbon sources. It is one of the few species of the genus candida which cause candidiasis in humans. 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. Fatty acids effect on lipase and biosurfactant induction in. The genus microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Heterogeneity of the genus has made its classification difficult with five varieties having been recognized. Whole genome sequencing and comparative genomic analysis. Molecular phylogenetics of the genus rhodotorula and related. 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. Rhodotorula species are pigmented basidiomycetous yeasts in the family sporidiobolaceae 21. Engineering an efficient and tight d amino acidinducible. 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.
The yeast strain cmgbrg5 was identified as rhodotorula glutinis using the biolog microlog system. 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. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091. Lipids accumulation in rhodotorula glutinis and cryptococcus curvatus growing on. Genome wide identification and evaluation of constitutive promoters in streptomycetes. Lifestyle, citing the centers for disease control and prevention.
Harrison is a pink glistening pucciniomycotina basidiomycota yeast species that is commonly isolated from air, freshwater and seawater all over the world. 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. Genetic analysis of dxylose metabolism by endophytic. Harrison, transactions of the royal society of canada. Race and transcriptomics showed that the cdna of acc1, acl1, fas1, fat1, dur1 and ldp1 contains a 5. Comparative analysis of protein families and genes. Draft genome sequences of both strains are reported here. Rhodotorula glutinis, rhodotorula minuta and rhodotorula mucilaginosa formerly known as. 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. Proteome analysis of xylose metabolism in rhodotorula. The genus contains 37 species, of which only three, including r.
Previously considered nonpathogenic, rhodotorula species have emerged as opportunistic pathogens that have the ability to colonise and infect susceptible patients. A molecular approach was applied to the study of the carotenoid biosynthetic pathway of rhodotorula mucilaginosa. The fungus is a common colonist of animals, foods and environmental materials. Genome assembly includes 62 contigs for a total of 22.
Therefore, it is vital to sequence the whole genome rhodotorula sp. 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. This is an updated paper focusing on the general epidemiological aspects of rhodotorula in humans, animals, and the environment. Engineering the oleaginous red yeast rhodotorula glutinis for. Draft genome sequence of rhodotorula mucilaginosa, an emergent. Mitochondrial genome was assembled separately and is available in the downloads section. Rhodotorula kratochvilovae strain ls11 is a biocontrol agent bca selected for its antagonistic activity against several plant pathogens both in the field and postharvest. Frontiers genome sequence of the plant growth promoting. Strain wp1 was isolated as an endophyte along with an assortment of bacteria within populus trichocarpa black cottonwood growing.
The engineering potential of rhodosporidium toruloides as. Candida auris is a species of fungus that grows as yeast. Microbotryum lychnidisdioicae infects silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Rhodotorula mucilaginosa assembly asm280678v1 download sequences in fasta format for genome. The strain selected for genome sequencing was isolated from the mycangia of sirex wasp in louisiana, usa. Introduction rhodotorula and rhodosporidium produce the major carotenoid pigments, carotene, torulene and torularhodin. Paul d, magbanua z, ma ii, french t, bridges sm, burgess sc, et al. Frontiers prospects for fungal bioremediation of acidic. Fast and efficient genetic transformation of oleaginous yeast. Engineering an efficient and tight damino acidinducible.
Car gene cluster and transcript levels of carotenogenic genes. Whole genome sequencing and comparative genomic analysis of. Genome sequence of the plant growth promoting endophytic yeast rhodotorula graminis wp1. At first, functional annotation of the genome of r. Pdf genome sequence of the oleaginous yeast rhodotorula. Pal phenylalanine ammonia lyase rhodotorula glutinis.
The rhodosporidium glutinis atcc 204091 was not sequenced or assembled at the doe joint genome institute. Developing a set of strong intronic promoters for robust. Publications genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091. Till now, two rhodotorula dao1 sequences have been deposited with genbank accession numbers.
Genome annotation predicts 7,642 proteinencoding genes. Three novel species, which are nonpathogenic to humans, have. Genome sequence of the plant growth promoting endophytic. In order to exclude the inherent quality of yeast, we added the model yeast s. High rhodotorula sequences in skin transcriptome of patients. Genetic transformation of the yeast rhodotorula gracilis. Then, a set of genes involved in different steps of carotenogenesis was identified and those coding for phytoene desaturase. Molecular phylogenetics of the genus rhodotorula and. To date, there is no effective method for inducible expression of proteins and rnas in these hosts. Rhodotorula mucilaginosa is a common saprophytic fungus that is a part of the basidiomycota phylum. Component name genome accessions component representation.
Systems used to automatically annotate proteins with high accuracy. This species has also been implicated in rare human infections. The current assembly of strain atcc 10788 comprises 61 scaffolds with a total size of 20. Integrative genomics viewer igv visualization of original read set to r. Wholegenome sequencing of an acidophilic rhodotorula sp. Whole genome sequencing of rhodotorula mucilaginosa. In present, there are studies describing the genome sequence of r. Fatty acids effect on lipase and biosurfactant induction. Dan close and john ojumu, draft genome sequence of the oleaginous yeast cryptococcus curvatus atcc 20509, genome announcements, 4, 6, e0123516, 2016.
Phylogenetic relationships of basidiomycetous yeasts, especially of the genus rhodotorula, were studied using partial sequences of the mitochondrial cytochrome b gene. Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Of the numerous species in the genus rhodotorula,onlyrhodotorula mucilaginosa,rhodotorula glutinis, andrhodotorula minuta. Rhodotorula glutinis an overview sciencedirect topics. Genome sequence of the oleaginous yeast rhodotorula glutinis atcc 204091 article pdf available january 2014 with 99 reads how we measure reads. Fast and efficient genetic transformation of oleaginous. Developing a set of strong intronic promoters for robust metabolic engineering in oleaginous rhodotorula rhodosporidium yeast species. 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. Cbs 20, ccrc 21418, ifo 1125, mucl 30253, nrrl y2502, ucd 68255, vkm y332 application. Lipids accumulation in rhodotorula glutinis and cryptococcus.
Rhodotorula toruloides is an outstanding producer of lipids and carotenoids. June 2016 the rhodotorula glutinis atcc 28052 genome was sequenced with illumina, assembled with allpathslg, and annotated with the jgi annotation pipeline. Crossref carlos rolz, two consecutive step process for ethanol and microbial oil production from sweet sorghum juice, biochemical engineering journal, 112, 186, 2016. Genome wide identification and evaluation of constitutive promoters in. Rhodotorula toruloides is a promising platform organism for production of lipids from lignocellulosic substrates. The upstream dna sequences of 6 genes involved in lipid biosynthesis or. Rhodotorula mucilaginosa jgtas1 genome sequencing project has been deposited in ncbi under. Rhodosporidium toruloides strain atcc 204091 iip 30 mtcc. This motivates us to perform a comparative genomic analysis between s. Microorganisms free fulltext rhodotorula mucilaginosa c2. 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. Oct 26, 2015 rhodosporidium and rhodotorula are two genera of oleaginous red yeast with great potential for industrial biotechnology. Engineering corynebacterium glutamicum for the production of 2,3butanediol engineering corynebacterium glutamicum for the production of 2,3butanediol.
Strain wp1 was isolated as an endophyte along with an assortment of bacteria within populus trichocarpa black cottonwood. Rhodosporidium glutinis atcc 204091 also known as rhodosporidium toruloides is a pinkcolored oleaginous fungus. Little is known about the metabolic aspects of lipid production from the lignocellolosic sugar xylose by oleaginous yeasts in general and r. 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. 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. Complete genome sequence of the biocontrol agent yeast. Whole genome sequencing of rhodotorula mucilaginosa isolated.
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. The engineering potential of rhodosporidium toruloides as a. High rhodotorula sequences in skin transcriptome of. Rhodotorula mucilaginosa jgtas1 genome sequencing project has been deposited in ncbi under bioproject prjna393004 and biosample. Unirule expertly curated rules saas system generated rules. 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. Rhodosporidium toruloides strain atcc 204091 iip 30. Compared to the lacking ballistospores rhodotorula toruloides and saccharomyces.
The ngr genome has predicted 5963 proteincoding genes, and the most of genes were annotated into the specie r. A limited number of rhodotorula species demonstrated identical sequences, for example rhodotorula bacarum and rhodotorula foliorum, rhodotorula fujisanensis and rhodotorula futronensis, rhodotorula glutinis var. Often, candidiasis is acquired in hospitals by patients with weakened immune systems. 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. Microorganisms free fulltext rhodotorula mucilaginosa. Here we show enrichment of rhodotorula sequences in the skin of patients with early, diffuse ssc compared with that in normal controls. Rhodotorula mucilaginosa, a yeast with valuable biotechnological features, has also been recorded as an emergent opportunistic. Given that rrna is present at much higher quantities than other transcripts, this is not unsurprising. Influence of cultural conditions on lipid production by mutant strain of rhodotorula glutinis mtcc 1151.
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