Draft Genome Sequence of the Oleaginous Yeast
            <i>Cryptococcus curvatus</i>
            ATCC 20509

Close, Dan; Ojumu, John O.

doi:10.1128/genomea.01235-16

Cited by 14 publications

(16 citation statements)

References 9 publications

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“…In this regard, transcriptome data can provide a good basis for predicting introns. We therefore collected transcriptome data (RNAseq) of C. oleaginosus ATCC 20509 from two conditions and used it to structurally annotate genome sequence MATS00000000.1 of C. oleaginosus ATCC 20509 [28].…”

Section: Resultsmentioning

confidence: 99%

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Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Pham

Reijnders

Suárez-Diez

et al. 2020

Preprint

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Abstract Background: Cutaneotrichosporon oleaginosus ATCC 20509 is a fast growing oleaginous basidiomycete yeast that is able to grow in a wide range of low-cost carbon sources including crude glycerol, a byproduct of biodiesel production. When glycerol is used as a carbon source, this yeast can accumulate more than 50% lipids (w/w) with high concentrations of mono-unsaturated fatty acids. Results: To increase our understanding of this yeast and to provide a knowledge base for further industrial use, a FAIR re-annotated genome was used to build a genome-scale, constraint-based metabolic model containing 1553 reactions involving 1373 metabolites in 11 compartments. A new description of the biomass synthesis reaction was introduced to account for massive lipid accumulation in conditions with high carbon to nitrogen (C/N) ratio in the media. This condition-speciﬁc biomass objective function is shown to better predict conditions with high lipid accumulation using glucose, fructose, sucrose, xylose and glycerol as sole carbon source. Conclusion: Contributing to the economic viability of biodiesel as renewable fuel, C. oleaginosus ATCC 20509 can eﬀectively convert crude glycerol waste streams in lipids as a potential bioenergy source. Performance simulations are essential to identify optimal production conditions and to develop and ﬁne tune a cost-eﬀective production process. Our model suggests ATP-citrate lyase as a target for further improve lipid production. Keywords: Genome-scale metabolic model; Cutaneotrichosporon oleaginosus ATCC 20509; lipid accumulation; Crude glycerol; biodiesel production; ﬂux balance analysis; oleaginous yeast

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Section: Resultsmentioning

confidence: 99%

“…The genome sequence MATS00000000.1 from Cutaneotrichosporon oleaginosus ATCC 20509 reported by [28] was annotated and used to build the model. The genome sequence has 19.86 Mbp and a GC content of 60.7%.…”

Section: Genome Sequencementioning

confidence: 99%

Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Pham

Reijnders

Suárez-Diez

et al. 2020

Preprint

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“…Since 2015, genome sequences have been published for Trichosporonales species from the genera Apiotrichum, Cutaneotrichosporon, Takashimella, Trichosporon, and Vanrija [45][46][47][48][49][50][51][52] ( Table 1). We analyzed the genomes of 29 isolates that belong to 24 Trichosporonales species for the organization of the MAT loci, and found that all of them contain fused MAT loci, with both mating-type determining genes (STE3 and SXI) located ~55 kb apart from each other.…”

Section: Trichosporonales Species Have Fused Hd and P/r Mating Type Locimentioning

confidence: 99%

“…Recently, several Trichosporonales were studied with respect to their biotechnological properties, including the oil-accumulating C. oleaginosum, which was first isolated from a dairy plant, and has the ability to metabolize chitin-rich and other nonconventional substrates [41][42][43][44]. The sequenced C. oleaginosum strain is haploid, and similar in genome size and gene content to genomes from the sister order Tremellales, and this was also the case for several other Trichosporonales genomes that have since been sequenced [43,[45][46][47][48][49][50]. Interestingly, C. oleaginosum showed some similarities to C. neoformans in the organization of MAT loci.…”

mentioning

confidence: 92%

“…A well-studied case of fused MAT loci is the one of Cryptococcus neoformans, a member of a group of closely related, pathogenic Cryptococcus species [1]. Fusion of the HD and P/R loci most likely occurred in the ancestor of the pathogenic Cryptococci, because other analyzed Tremellales species including the closely related, but non-pathogenic Cryptococcus Since the analysis of the first C. oleaginosum genome, several more Trichosporonales genomes were sequenced, although none were analyzed with respect to their MAT loci [45][46][47][48][49][50][51]. Here, we describe the sequencing of two additional Trichosporonales genomes for C. oleaginosum ATCC20508 and Vanrija humicola CBS4282, and the analysis of MAT loci organization in Trichosporonales genomes from 24 different species.…”

Section: Introductionmentioning

confidence: 99%

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Convergent evolution of linked mating-type loci in basidiomycete fungi

Sun

Coelho

Heitman

et al. 2019

Preprint

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Author summarySexual development in fungi is governed by mating-type (MAT) genes, and the corresponding MAT loci show similarities to sex chromosomes in animals and plants. One common feature is an evolutionary trend towards combining sex-associated genes on the same chromosome, which can evolve by selection because it facilitates linkage of favorable allele combinations.Here, we show that this occurred in the Trichosporonales, a sister group to the Tremellales, similar to the expanded, fused MAT loci discovered previously in the human pathogen Cryptococcus neoformans. Our data suggest that fusion of MAT loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions in fungi. amylolentus, Kwoniella heveanensis, Kwoniella mangrovensis, Cryptococcus wingfieldii, andCryptococcus floricola are all tetrapolar [29][30][31][32][33]. The fused C. neoformans MAT locus encompasses more than 20 genes over a region spanning more than 100 kb and has two alleles designated a and . In the majority of basidiomycetes, each MAT allele at the HD locus carries both the HD1 and the HD2 transcription factor genes, whereas in C. neoformans, the MAT locus contains only the HD1 gene SXI1, and MATa contains only the HD2 gene SXI2a. Except for a gene conversion hotspot, the C. neoformans MAT locus displays suppressed meiotic recombination [23,34,35].Among the Tremellomycetes, pathogenic Cryptococci are so far the only species for which fused MAT loci have been described [17,23]. In a previous study, we analyzed the genome sequence of Cutaneotrichosporon oleaginosum strain IBC0246 (formerly Trichosporon oleaginosus), which belongs to the Trichosporonales, a sister order to the Tremellales within the Tremellomycetes class. Trichosporonales species are widely distributed in the environment and have been isolated from a variety of substrates including soil, decaying plant material, and water. Many species are saprobes, but some have also been found to be associated with animals including humans either as commensals or pathogens [36][37][38].Despite their common occurrence in the environment, Trichosporonales are an understudied fungal group, and sexual reproduction has not yet been observed for any of the known species [39,40]. Recently, several Trichosporonales were studied with respect to their biotechnological properties, including the oil-accumulating C. oleaginosum, which was first isolated from a dairy plant, and has the ability to metabolize chitin-rich and other nonconventional substrates [41][42][43][44]. The sequenced C. oleaginosum strain is haploid, and similar in genome size and gene content to genomes from the sister order Tremellales, and this was also the case for several other Trichosporonales genomes that have since been sequenced [43,[45][46][47][48][49][50]. Interestingly, C. oleaginosum showed some similarities to C. neoformans in the organization of MAT loci. This included recruitment of genes with diverse functions during mati...

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Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

et al. 2022

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The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

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Draft Genome Sequence of the Oleaginous Yeast Cryptococcus curvatus ATCC 20509

Cited by 14 publications

References 9 publications

Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Convergent evolution of linked mating-type loci in basidiomycete fungi

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

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