Genome Anatomy of <i>Pyrenochaeta unguis-hominis</i> UM 256, a Multidrug Resistant Strain Isolated from Skin Scraping

<div><p><i>Pyrenochaeta unguis-hominis</i> is a rare human pathogen that causes infection in human skin and nail. <i>P</i>. <i>unguis-hominis</i> has received little attention, and thus, the basic biology and pathogenicity of this fungus is not fully understood. In this study, we performed in-depth analysis of the <i>P</i>. <i>unguis-hominis</i> UM 256 genome that was isolated from the skin scraping of a dermatitis patient. The isolate was identified to species level using a comprehensive multilocus phylogenetic analysis of the genus <i>Pyrenochaeta</i>. The assembled UM 256 genome has a size of 35.5 Mb and encodes 12,545 putative genes, and 0.34% of the assembled genome is predicted transposable elements. Its genomic features propose that the fungus is a heterothallic fungus that encodes a wide array of plant cell wall degrading enzymes, peptidases, and secondary metabolite biosynthetic enzymes. Antifungal drug resistance genes including <i>MDR</i>, <i>CDR</i>, and <i>ERG11/CYP51</i> were identified in <i>P</i>. <i>unguis-hominis</i> UM 256, which may confer resistance to this fungus. The genome analysis of <i>P</i>. <i>unguis-hominis</i> provides an insight into molecular and genetic basis of the fungal lifestyles, understanding the unrevealed biology of antifungal resistance in this fungus.</p></div

<i>MAT1-2-1</i> gene of <i>P</i>. <i>unguis-hominis</i> UM256.

<p>Genes constituting the MAT locus: <i>MAT1-2-1</i> (UM256_7301), DNA lyase, <i>Apn2</i> (UM 256_7302) and cytochrome C oxidase subunit Vla, <i>Cox13</i> (UM256_7303).</p

List of <i>Pyrenochaeta</i> spp. fungus sequences (ITS, SSU, and LSU) obtained from NCBI and Q-bank for phylogenetic trees.

<p>List of <i>Pyrenochaeta</i> spp. fungus sequences (ITS, SSU, and LSU) obtained from NCBI and Q-bank for phylogenetic trees.</p

Bayesian phylogenetic tree of <i>Pyrenochaeta</i> sp. based on the combined genes of ITS, SSU and LSU sequenced data.

<p>The phylogenetic tree were constructed with 12 <i>Pyrenochaeta</i> species. The tree is rooted with <i>C</i>. <i>hispidulum</i> and <i>S</i>. <i>terrestris</i> as outgroup. The numbers on the nodes indicate Bayesian posterior probabilities.</p

Amino acid substitution detected in <i>ERG 11/CYP51</i> genes of <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>Amino acid substitution detected in <i>ERG 11/CYP51</i> genes of <i>P</i>. <i>unguis-hominis</i> UM 256.</p

Phylogenomic analysis of <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>The phylogenomic tree was constructed with total of 23 fungi including four from Sordariomycetes, nine from Dothideomycetes, eight from Eurotiomycetes and two outgroups from the Saccharomycetes (<i>C</i>. <i>albicans</i> and <i>S</i>. <i>cerevisiae</i>).</p

KOG and KEGG classifications of proteins in <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>(A) KOG class annotation distribution of <i>P</i>. <i>unguis-hominis</i> UM 256 genome. A: RNA processing and modification; B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Post-translational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; W: Extracellular structures; X: Unnamed protein and Z: Cytoskeleton. (B) Distribution of predicted proteins from <i>P</i>. <i>unguis-hominis</i> UM 256 genome that involved in metabolic pathway by KEGG database.</p

Peptidase and genes that involved in keratin degradation of <i>P</i>. <i>unguis-hominis</i> UM 256.

<p>Peptidase and genes that involved in keratin degradation of <i>P</i>. <i>unguis-hominis</i> UM 256.</p

CAZymes class distribution of <i>P</i>. <i>unguis-hominis</i> and others Dothideomycetes.

<p>(A) Distribution of each of the CAZymes family among <i>P</i>. <i>unguis-hominis</i> UM 256 and other Dohideomycetes fungi. (B) Distribution of CAZymes family involved in plant cell wall degradation. (C) Auxiliary group (AA) of CAZymes distribution among <i>P</i>. <i>unguis-hominis</i> UM 256 and others Dothideomycetes fungi. AA, auxiliary activities; CBM, carbohydrate-binding modules; CE, carbohydrate esterases; GH, glycoside hydrolases; GT, glycosyltransferases; PL, polysaccharide lyases. C, cellulose; H, Hemicellulose; P, pectin; HP, enzymes that degrade hemicellulose of pectin side chain.</p

Primers and gene size (bp) of antifungal resistance genes that used for PCR amplification.

<p>Primers and gene size (bp) of antifungal resistance genes that used for PCR amplification.</p