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

Abstract

Summary 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.

Phylogenetic Diversity, Host Specificity, and Distribution of the Wood-Decaying Fungus Phellinotus teixeirae in Western Colombia’s Seasonally Dry Tropical Forest

“…These levels of nucleotide diversity could, in turn, harness species delimitation between the closely related taxa P. piptadeniae and P. teixeirae. Similarly, the high nucleotide diversity found in P. piptadeniae indicates that clusters of divergent sequences occur within the species, possibly as a consequence of geographic distance, environmental local adaptation (considering its disjunct distribution [1]), divergent host interactions, or ancient intraspecific rDNA polymorphisms [57,58]. For P. teixeirae, the nucleotide variation was very low between our isolates and previous reports, despite the new host interactions with Pithecellobium dulce.…”

“…For P. teixeirae, the nucleotide variation was very low between our isolates and previous reports, despite the new host interactions with Pithecellobium dulce. These contrasting outcomes have been identified in eukaryotic genomes [59][60][61][62][63], particularly coupled with considerable variation in gene copy number at rDNA loci in fungal species [57,58,64,65] and intragenomic variation at these loci [58,64,65]. The dynamics of these variations complicate the analysis of rDNA amplicons, being a critical factor for species delimitation, especially for microbial communities in heterogeneous environments [6].…”