Draft Genome Sequence of CBS 2479, the Standard Type Strain of Trichosporon asahii

Yang, Rong; Li, Hai Tao; Zhu, He; Zhou, Guangpeng; Wang, Meng; Wang, Lei

doi:10.1128/ec.00237-12

Cited by 16 publications

(21 citation statements)

References 11 publications

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“…Libraries were Nextera® DNA Library Preparation Kit and sequencing using a 2 × 150 nucleotide paired‐end strategy. Library adaptators of paired‐ends read were trimmed with Cutadapt version 1.18 (https://doi.org/10.14806/ej.17.1.200) and then mapped to the 78 scaffolds of the reference genome of CBS2479 23 (GenBank accession number ) using the Burrows‐Wheeler Alignment tool, BWA version 0.7.13 29 with the BWA‐mem algorithm. SAMtools version 1.9 and Picard tools version 1.94 (http://broadinstitute.github.io/picard) were then used to filter, sort, convert SAM files and assign read groups and mark duplicate reads.…”

Section: Methodsmentioning

confidence: 99%

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Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Desnos‐Ollivier

Maufrais

Pihet

et al. 2020

Mycoses

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Summary Background Trichosporonosis is a rare invasive infection in humans mainly due to Trichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. Objectives We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. Methods IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. Results All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs‐old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked. Conclusions We confirmed the usefulness of IGS1 sequencing for grouped cases infection of T. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.

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Section: Methodsmentioning

confidence: 99%

“…Other haplotypes are described in Spain, Japan and Brazil 20,21 . In 2012, Yang et al sequenced the whole genome of two strains of T. asahii (an environmental isolate, CBS8904, recovered from maize cobs, in 1998, Illinois, USA 22 and a clinical isolate, CBS2479, the type strain, recovered in Japan in 1929 from a psoriasis lesion) 23 …”

Section: Introductionmentioning

confidence: 99%

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Desnos‐Ollivier

Maufrais

Pihet

et al. 2020

Mycoses

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“…the species option was ‘cryptococcus’). For GeneMark, the gene model was trained using data from the Trichosporon asahii CBS 2479 genome (Yang et al, ). In both cases, only complete genes coding for at least 100 amino acid residues were included.…”

Section: Methodsmentioning

confidence: 99%

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved ‘natural’ hybrid genomes

Takashima

Sriswasdi

Manabe³

et al. 2017

Yeast

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To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd.

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“…The perfectfrombam module was run with the following parameters: min insert = 100, max insert = 500, repetitive max qual = 3, perfect min qual = 4, and perfect min alignment score = 150. For T. asahii, the published genome for strain CBS 2479 (Yang et al 2012) was used. The genome sequence data was also used in a separate study that focuses on fungal systematics (Takashima et al 2015).…”

Section: Methodsmentioning

confidence: 99%

“…We sequenced the genomes of Trichosporon coremiiforme, T. faecale, T. inkin, and T. ovoides and downloaded that of T. asahii strain CBS2479 (Supplemental Table S1; Yang et al 2012). The genome sizes of T. coremiiforme and T. ovoides (40)(41)(42) relative to those of closely related T. asahii, T. faecale, and T. inkin (20)(21)(22)(23)(24)(25) suggested that these two species experienced recent genome expansions.…”

Section: Recent and Independent Genome Hybridizations In Trichosporonmentioning

confidence: 99%

Global deceleration of gene evolution following recent genome hybridizations in fungi

Sriswasdi

Takashima

Manabe³

et al. 2016

Genome Res.

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Polyploidization events such as whole-genome duplication and inter-species hybridization are major evolutionary forces that shape genomes. Although long-term effects of polyploidization have been well-characterized, early molecular evolutionary consequences of polyploidization remain largely unexplored. Here, we report the discovery of two recent and independent genome hybridizations within a single clade of a fungal genus, Trichosporon. Comparative genomic analyses revealed that redundant genes are experiencing decelerations, not accelerations, of evolutionary rates. We identified a relationship between gene conversion and decelerated evolution suggesting that gene conversion may improve the genome stability of young hybrids by restricting gene functional divergences. Furthermore, we detected large-scale gene losses from transcriptional and translational machineries that indicate a global compensatory mechanism against increased gene dosages. Overall, our findings illustrate counteracting mechanisms during an early phase of post-genome hybridization and fill a critical gap in existing theories on genome evolution. [Supplemental material is available for this article.]Polyploidization events such as whole-genome duplication (WGD) and inter-species hybridization are major evolutionary forces that shape eukaryotic genomes (Dehal and Boore 2005;Scannell et al. 2007;Sémon and Wolfe 2007;Jaillon et al. 2009; Van de Peer et al. 2009). Ohno (1970 proposed an important theory that explains the enhanced evolutionary capability of polyploid genomes, stating that the emergence of functionally redundant genes would relax their evolutionary constraints and accelerate divergent evolution of their functions. This theory has been confirmed in a wide range of eukaryotes from ancient Vertebrata (Brunet et al. 2006), Saccharomycetaceae fungi (Kellis et al. 2004;Byrne and Wolfe 2007), Paramecia (McGrath et al. 2014), and Brassicaceae plants (Arabidopsis Genome Initiative 2000;Vision et al. 2000). Nonetheless, although these studies established long-term benefits of polyploidization, early consequences and mechanisms of polyploidization remain largely unexplored.Genome hybridization, in contrast to WGD, which is a rare event, is estimated to occur in >25% of plant and 10% of animal species (Mallet 2005) and generally involves younger species. In fungi, a multitude of hybrids have given rise to species that are instrumental in industrial fermentation and critical plant and animal pathogens. Furthermore, in addition to the issue of globally increased gene dosage that is common between WGD and genome hybridization, a hybrid species has to resolve the issue of incompatible genes and proteins encoded by its two parental genomes. Recent analyses of several fungal hybrids have revealed mechanisms such as extensive loss of heterozygosity Louis et al. 2012;Stukenbrock et al. 2012) and gene expression reprogramming (Tirosh et al. 2009) that may help hybrid genomes stabilize. Gene conversion, which is capable of homogenizing redundant paralogs...

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Draft Genome Sequence of CBS 2479, the Standard Type Strain of Trichosporon asahii

Cited by 16 publications

References 11 publications

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

Epidemiological investigation for grouped cases of Trichosporon asahii using whole genome and IGS1 sequencing

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved ‘natural’ hybrid genomes

Global deceleration of gene evolution following recent genome hybridizations in fungi

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