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Comparative Genomic Analysis of an Apiotrichum cacaoliposimilis Strain Isolated from a Patient with Urinary Tract Infection

Wei Wang

Wei Wang

  • Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
  • Department of Public Health, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Wang, Wei
, 
Jinping Yi

Jinping Yi

Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Yi, Jinping
, 
Jiahuan Zhan

Jiahuan Zhan

  • Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
  • Department of Public Health, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Zhan, Jiahuan
, 
Dong Luo

Dong Luo

Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Luo, Dong
, 
Qiang Chen

Qiang Chen

Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Chen, Qiang
, 
Shengming Yu

Shengming Yu

  • Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
  • Department of Public Health, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Yu, Shengming
, 
Ling Xie

Ling Xie

  • Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
  • Department of Public Health, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Xie, Ling
 and 
Kaisen Chen

Kaisen Chen

Department of Clinical Laboratory, the First Affiliated Hospital, Jiangxi Medical College, Nanchang UniversityNanchang, China
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Chen, Kaisen
  
Dec 13, 2024
Comparative Genomic Analysis of an Apiotrichum cacaoliposimilis Strain Isolated from a Patient with Urinary Tract Infection's Cover Image
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Article Category: ORIGINAL PAPER
Published Online: Dec 13, 2024
Page range: 475 - 489
Received: Jun 18, 2024
Accepted: Sep 12, 2024
DOI: https://doi.org/10.33073/pjm-2024-038
Keywords
© 2024 Wei Wang et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
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Fig. 1.

Morphology of the UB0827 strain: A) image after incubation on Sabouraud’s medium for 3 days; B) Gram staining under the microscope (1000× magnification); C) lactophenol cotton blue staining under the microscope (1000× magnification); D) hexamethylamine silver staining under the microscope (1000× magnification); E) fluorescent staining under the microscope (1000 magnification). Black arrows indicate the fungal filaments. Yellow arrows indicate the potential arthrospores. Red arrows indicate the budding spores.
Morphology of the UB0827 strain: A) image after incubation on Sabouraud’s medium for 3 days; B) Gram staining under the microscope (1000× magnification); C) lactophenol cotton blue staining under the microscope (1000× magnification); D) hexamethylamine silver staining under the microscope (1000× magnification); E) fluorescent staining under the microscope (1000 magnification). Black arrows indicate the fungal filaments. Yellow arrows indicate the potential arthrospores. Red arrows indicate the budding spores.

Fig. 2.

The legend on the right side of the figure lists the functional classifications of the Gene Ontology (GO) annotations for the corresponding samples under the three categories of GO ontology classifications. The left side of the figure depicts the distribution of a number of GO functional analyses on the annotations. The horizontal axis represents the number of genes, displayed in different colors corresponding to the different types mentioned in the legend on the right. The vertical axis presents the GO functional classification.
The legend on the right side of the figure lists the functional classifications of the Gene Ontology (GO) annotations for the corresponding samples under the three categories of GO ontology classifications. The left side of the figure depicts the distribution of a number of GO functional analyses on the annotations. The horizontal axis represents the number of genes, displayed in different colors corresponding to the different types mentioned in the legend on the right. The vertical axis presents the GO functional classification.

Fig. 3.

A phylogenomic analysis of the thirty-seven members of the Trichosporonaceae family, conducted using the maximum likelihood (ML) method. The ML tree was constructed based on the concatenated non-gapped sites from multiple whole-genome alignments. The branch length of this tree represented the evolutionary distance on the tree scale. The phylogenetic analysis was conducted using raxmlHPC-PTHREADS-AVX (v8.2.13), utilizing the GTRGAMMA model and 1,000 bootstrap replicates. The genera Apiotrichum, Trichosporon, Cutaneotrichosporon, and Vanrija within the Trichosporonaceae family and the genus Takashimella (outgroup) in Tetragoniomycetaceae are highlighted in red, gray, yellow, green, and blue, respectively.
A phylogenomic analysis of the thirty-seven members of the Trichosporonaceae family, conducted using the maximum likelihood (ML) method. The ML tree was constructed based on the concatenated non-gapped sites from multiple whole-genome alignments. The branch length of this tree represented the evolutionary distance on the tree scale. The phylogenetic analysis was conducted using raxmlHPC-PTHREADS-AVX (v8.2.13), utilizing the GTRGAMMA model and 1,000 bootstrap replicates. The genera Apiotrichum, Trichosporon, Cutaneotrichosporon, and Vanrija within the Trichosporonaceae family and the genus Takashimella (outgroup) in Tetragoniomycetaceae are highlighted in red, gray, yellow, green, and blue, respectively.

Fig. 4.

A) Venn diagram illustrating the relationships between A. cacaoliposimilis UB0827 and the different Trichosporonaceae genera based on the 6656 orthogroups; B) Venn diagram illustrating the relationships among different species positioned on the same node.
A) Venn diagram illustrating the relationships between A. cacaoliposimilis UB0827 and the different Trichosporonaceae genera based on the 6656 orthogroups; B) Venn diagram illustrating the relationships among different species positioned on the same node.

Fig. 5.

The synteny analysis performed at the genomic level for strain UB0827 and the representative strains of different nodes. The number displayed between the strains indicates the number of syntenic blocks, which become increasingly dense when moving from top to bottom. The straight line exists due to the poor assembly quality of the HP2023 strain.
The synteny analysis performed at the genomic level for strain UB0827 and the representative strains of different nodes. The number displayed between the strains indicates the number of syntenic blocks, which become increasingly dense when moving from top to bottom. The straight line exists due to the poor assembly quality of the HP2023 strain.

Fig. 6.

A) The outermost circle represents the chromosome skeleton, with strain GMU1709 depicted in green and strain UB0827 depicted in light grey. The inner circle indicates gene density, with a gradient from white to blue indicating an increase in the number of genes. Syntenic pairs indicate the shared pathogenic genes. The genes depicted on the left skeleton are shared genes, while the genes depicted on the right skeleton are the genes specific to A. cacaoliposimilis. The colors of the genes indicate their respective phenotypic classifications. B) A total of 77 disease-causing genes are depicted, with 72 of these genes differing between the various genera and 5 genes differing between species. The outermost color on the left corresponds to the grouping, while the innermost color represents the phenotypic classification of the disease-causing genes. The top hints at the origin of the isolated strain. The gradient from dark blue to yellow indicates an increase in the number of genes.
A) The outermost circle represents the chromosome skeleton, with strain GMU1709 depicted in green and strain UB0827 depicted in light grey. The inner circle indicates gene density, with a gradient from white to blue indicating an increase in the number of genes. Syntenic pairs indicate the shared pathogenic genes. The genes depicted on the left skeleton are shared genes, while the genes depicted on the right skeleton are the genes specific to A. cacaoliposimilis. The colors of the genes indicate their respective phenotypic classifications. B) A total of 77 disease-causing genes are depicted, with 72 of these genes differing between the various genera and 5 genes differing between species. The outermost color on the left corresponds to the grouping, while the innermost color represents the phenotypic classification of the disease-causing genes. The top hints at the origin of the isolated strain. The gradient from dark blue to yellow indicates an increase in the number of genes.
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Antifungal susceptibility of Apiotrichum cacaoliposimilis UB0827_

Antifungal susceptibility (MICs, μg/ml)
5FC AMB FLU POS VOR ITZ ANID MICA CASP
2 0.5 2 0.06 0.06 0.12 8 8 8

The following are the different/important biochemical reactions between strains Apiotrichum cacaoliposimilis UB0827, ATCC® 20505™ and Apiotrichum mycotoxinovorans GMU1709_

Biochemical reaction Strain
UB0827 ATCC® 20505™ GMU1709
L-lysine-arylamidase − + −
Erythritol assimilation − − −
Glycerol assimilation − + +
β-N-Acetyl-glucosaminidase − + +
Arbutin assimilation − + −
Methyl-α-D-glucopyranoside assimilation − + −
D-Raffinose assimilation − − +
PNP-N-acetyl-β-D-galactosaminidase 1 − − +
D-Melibiose assimilation − D +
D-Melezitose assimilation − + −
L-Sorbose assimilation − + −
Xylitol assimilation − + −
D-Sorbitol assimilation − / +
Urease + + +
D-Trehalose assimilation + + +
Nitrate assimilation − + +
D-Galacturonate assimilation + − +
Esculin hydrolysis − / +
DL-Lactate assimilation + − +
Citrate (sodium) assimilation − D/W +
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