Draft Genome Sequence of the Causative Antigen of Summer-Type Hypersensitivity Pneumonitis,
            <i>Trichosporon domesticum</i>
            JCM 9580

Cho, Otomi; Ichikawa, Tomoe; Kurakado, Sanae; Takashima, Masako; Manabe, Ri-ichiroh; Ohkuma, Moriya; Sugita, Takashi

doi:10.1128/genomea.00651-16

Cited by 6 publications

(9 citation statements)

References 16 publications

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“…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 non-conventional substrates [44][45][46][47]. The sequenced C. oleaginosum strain is haploid and similar in genome size and gene content to strains from the sister order Tremellales; this is also the case for several other Trichosporonales genomes that have since been sequenced [28,46,[48][49][50][51][52]. Interestingly, C. oleaginosum showed some similarities to C. neoformans in the organization of MAT loci.…”

Section: Introductionmentioning

confidence: 93%

“…Since the analysis of the first C. oleaginosum genome, several more Trichosporonales genomes have been sequenced, although none were analyzed with respect to their MAT loci [28,[48][49][50][51][52][53]. 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

et al. 2019

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Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In basidiomycetes, the ancestral state is hypothesized to be tetrapolar, with two genetically unlinked MAT loci containing homeodomain transcription factor genes (HD locus) and pheromone and pheromone receptor genes (P/R locus), respectively. Alleles at both loci must differ between mating partners for completion of sexual development. However, there are also basidiomycetes with bipolar mating systems, which can arise through genomic linkage of the HD and P/R loci. In the order Tremellales, bipolarity is found only in the pathogenic Cryptococcus species. Here, we describe the analysis of MAT loci from 24 species of the Trichosporonales, a sister order to the Tremellales. In all of the species analyzed, the MAT loci are fused and a single HD gene is present in each mating type, similar to the organization in the pathogenic Cryptococci. However, the HD and P/R allele combinations in the Trichosporonales are different from those in the pathogenic Cryptococci. This and the existence of tetrapolar species in the Tremellales suggest that fusion of the HD and P/R loci occurred independently in the Trichosporonales and pathogenic Cryptococci, supporting the hypothesis of convergent evolution towards fused MAT regions, similar to previous findings in other fungal groups. Unlike the fused MAT loci in several other basidiomycete lineages though, the gene content and gene order within the fused MAT loci are highly conserved in the Trichosporonales, and there is no apparent suppression of recombination extending from the MAT loci to adjacent chromosomal regions, suggesting different mechanisms for the evolution of physically linked MAT loci in these groups.

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Section: Introductionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Convergent evolution of linked mating-type loci in basidiomycete fungi

et al. 2019

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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

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Coelho

Heitman

et al. 2019

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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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Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes

2017

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The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects.

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Draft Genome Sequence of the Causative Antigen of Summer-Type Hypersensitivity Pneumonitis, Trichosporon domesticum JCM 9580

Abstract: Here, we report the draft genome sequence of Trichosporon domesticum JCM 9580, isolated from the house of a patient with summer-type hypersensitivity pneumonitis (SHP) in Japan. This genomic information will help elucidate the mechanisms of the development of SHP.

Cited by 6 publications

References 16 publications

Convergent evolution of linked mating-type loci in basidiomycete fungi

Convergent evolution of linked mating-type loci in basidiomycete fungi

Convergent evolution of linked mating-type loci in basidiomycete fungi

Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes

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