Dataset Information

Variations in ribosomal DNA copy numbers in a genome of Trichophyton interdigitale.

ABSTRACT: BACKGROUND:Ribosomal DNA (rDNA) reportedly has multiple copies in the fungal genome. The internal transcribed spacer (ITS) region in rDNA is useful for investigating relationships between close taxonomic relatives. Thus, ITS has been widely used as a target gene in medical mycology for the detection of pathogenic fungi and identification of fungal species. However, the rDNA copy number in a genome of Trichophyton interdigitale, the pathogen causing dermatophytosis, currently remains unknown. OBJECTIVE:Clarification of the rDNA copy number in a genome of T. interdigitale. METHODS:rDNA copy numbers in 64 clinical isolates of T. interdigitale were examined using quantitative real-time PCR (qPCR) with the absolute quantitative method targeting TruMDR2, a single-copy control gene and the ITS region in rDNA. RESULTS:The copy numbers of the rDNA subunit varied among the 64 strains tested, from 24 to 116 copies per genome. The average rDNA copy number ± standard deviation was 59 ± 16. No correlations were observed between the rDNA copy number and colony colour, colony morphology or molecular type of the non-transcribed spacer region in rDNA. Experiments on rDNA copy numbers obtained from independent colonies of each strain in single-spore cultures revealed that the copy number was homogeneous within each strain. CONCLUSION:This is the first study to estimate copy numbers of the rDNA subunit in a genome of T. interdigitale. The rDNA copy number of T. interdigitale varied among the strains tested and was homogeneous within each strain.

SUBMITTER: Iwanaga T

PROVIDER: S-EPMC7607385 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Variations in ribosomal DNA copy numbers in a genome of Trichophyton interdigitale.

Iwanaga Tomoyuki T Anzawa Kazushi K Mochizuki Takashi T

Mycoses 20200902 10

<h4>Background</h4>Ribosomal DNA (rDNA) reportedly has multiple copies in the fungal genome. The internal transcribed spacer (ITS) region in rDNA is useful for investigating relationships between close taxonomic relatives. Thus, ITS has been widely used as a target gene in medical mycology for the detection of pathogenic fungi and identification of fungal species. However, the rDNA copy number in a genome of Trichophyton interdigitale, the pathogen causing dermatophytosis, currently remains unkn ...[more]

PMID: 32783279

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Project description:Somatic mosaicism denotes the presence of genetically distinct populations of somatic cells in one individual who has developed from a single fertilised oocyte. Mosaicism may result from a mutation that occurs during postzygotic development and is propagated to only a subset of the adult cells. Our aim was to investigate both somatic mosaicism for copy-neutral loss of heterozygosity (cn-LOH) events and DNA copy number variations (CNVs) in fully differentiated tissues.We studied panels of tissue samples (11-12 tissues per individual) from four autopsy subjects using high-resolution Illumina HumanOmniExpress-12 BeadChips to reveal the presence of possible intra-individual tissue-specific cn-LOH and CNV patterns. We detected five mosaic cn-LOH regions >5 Mb in some tissue samples in three out of four individuals. We also detected three CNVs that affected only a portion of the tissues studied in one out of four individuals. These three somatic CNVs range from 123 to 796 kb and are also found in the general population. An attempt was made to explain the succession of genomic events that led to the observed somatic genetic mosaicism under the assumption that the specific mosaic patterns of CNV and cn-LOH changes reflect their formation during the postzygotic embryonic development of germinal layers and organ systems.Our results give further support to the idea that somatic mosaicism for CNVs, and also cn-LOHs, is a common phenomenon in phenotypically normal humans. Thus, the examination of only a single tissue might not provide enough information to diagnose potentially deleterious CNVs within an individual. During routine CNV and cn-LOH analysis, DNA derived from a buccal swab can be used in addition to blood DNA to get information about the CNV/cn-LOH content in tissues of both mesodermal and ectodermal origin. Currently, the real frequency and possible phenotypic consequences of both CNVs and cn-LOHs that display somatic mosaicism remain largely unknown. To answer these questions, future studies should involve larger cohorts of individuals and a range of tissues.

Dataset Information

Variations in ribosomal DNA copy numbers in a genome of Trichophyton interdigitale.

Publications

Variations in ribosomal DNA copy numbers in a genome of Trichophyton interdigitale.

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