Comparative genomic and phenotypic analyses of pathogenic fungi Neoscytalidium dimidiatum and Bipolaris papendorfii isolated from human skin scraping

Abstract

Neoscytalidium dimidiatum and Bipolaris species are fungal plant pathogens that have been reported to cause human diseases. Recently, we have isolated numerous N. dimidiatum and Bipolaris species from the skin scrapings and nails of different patients. In this work, we have sequenced the genome of one strain of N. dimidiatum. The sequenced genome was compared to that of a previously reported Bipolaris papendorfii genome for a better understanding of their complex lifestyle and broad host-range pathogenicity. Both N. dimidiatum UM 880 (~ 43 Mb) and B. papendorfii UM 226 (~ 33 Mb) genomes include 11,015-12,320 putative coding DNA sequences, of which 0.51-2.49% are predicted transposable elements. Analysis of secondary metabolism gene clusters revealed several genes involved in melanin biosynthesis and iron uptake. The arsenal of CAZymes related to plants pathogenicity is comparable between the species, including genes involved in hemicellulose and pectin decomposition. Several important gene encoding keratinolytic peptidases were identified in N. dimidiatum and B. papendorfii, reflecting their potential pathogenic role in causing skin and nail infections. In this study, additional information on the metabolic features of these two species, such as nutritional profiling, pH tolerance, and osmotolerant, are revealed. The genomic characterization of N. dimidiatum and B. papendorfii provides the basis for the future functional studies to gain further insights as to what makes these fungi persist in plants and why they are pathogenic to humans.

Keywords: Bipolaris papendorfii; Dematiaceous; Fungal plant pathogen; Neoscytalidium dimidiatum; Skin scraping.

Fig. 1

Macroscopic and microscopic morphology of N. dimidiatum UM 880. The surface (A), close-up (B), and reverse (C) view of colony morphology of N. dimidiatum UM 880 after being cultured for 7 days on SDA. Lactophenol cotton blue mount showing D typical arthroconidia of N. dimidiatum (× 400 magnification, bars 20 µm). Two-celled conidia are also shown (arrows). Scanning electron micrograph showing E the arthroconidia were cylindrical with smooth to slightly verruculose walled and arranged in chains

Fig. 2

KOG and KEGG classifications of proteins in N. dimidiatum UM 880 and B. papendorfii UM 226. A KOG class annotation distribution of N. dimidiatum UM 880 and B. papendorfii UM 226 genomes. 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 N. dimidiatum UM 880 and B. papendorfii UM 226 genomes that are involved in metabolic pathways by KEGG database

Fig. 3

Melanin biosynthetic genes identified in N. dimidiatum UM 880 and B. papendorfii UM 226 genomes. A Schematic representation of the biosynthetic gene cluster for the PKS in N. dimidiatum UM 880 and B. papendorfii UM 226 genomes. Numbers are in kilobases. B Domain analysis of NDPKS1, BPPKS1, and Bipolaris oryzae PKS1

Fig. 4

CAZyme class annotation distribution of N. dimidiatum UM 880 and B. papendorfii UM 226 genomes. A Comparison of the distribution of CAZyme catalytic domains between N. dimidiatum UM 880, B. papendorfii UM 226, and fungi from various lifestyles. CBM, carbohydrate binding module; CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyltransferase; PL, polysaccharide lyase. B Comparison of the plant cell wall degrading potential from CAZyme analysis between N. dimidiatum UM 880, B. papendorfii UM 226 and fungi from various lifestyles

Fig. 5

Mycelial growth of B. papendorfii UM 226 and N. dimidiatum UM 880 at pH 3.5–10. Results are expressed as mean ± standard error; n = 2. The means of B. papendorfii UM 226 and N. dimidiatum UM 880 were significantly different (p < 0.05; independent T-test) at each pH

Fig. 6

Mycelial growth of B. papendorfii UM 226 and N. dimidiatum UM 880 in media (pH 9.5) containing various nitrogenous sources. Results are expressed as mean from two independent runs. Control represents media (pH 9.5) without supplementation. ^ab means for B. papendorfii UM 226 with different lowercase letters are significantly different (p < 0.05; ANOVA with Tukey’s post hoc test). ^A means for N. dimidiatum UM 880 are not significantly different (p < 0.05; ANOVA with Tukey’s post hoc test)

Fig. 7

Mycelial growth of B. papendorfii UM 226 and N. dimidiatum UM 880 in media (pH 4.5) containing various nitrogenous sources. Results are expressed as mean from two independent runs. Control represent media (pH 4.5) without supplementation. ^abcdefgh means for B. papendorfii UM 226 with different lowercase letters are significantly different (p < 0.05; ANOVA with Tukey’s post hoc test). ^AB means for N. dimidiatum UM 880 with different uppercase letters are significantly different (p < 0.05; ANOVA with Tukey’s post hoc test)

Fig. 8

Mycelial growth of B. papendorfii UM 226 and N. dimidiatum UM 880 in solution containing various concentration of NaCl. Results are expressed as mean ± standard error; n = 2. The means of B. papendorfii UM 226 and N. dimidiatum UM 880 were significantly different (p < 0.05; independent T-test) at each concentration of NaCl

Fig. 9

Mycelial growth of B. papendorfii UM 226 () and N. dimidiatum UM 880 () in media containing 6% NaCl and supplemented with various osmolytes. Results are expressed as mean from two independent runs. Control represent media containing 6% NaCl only. ^abcd means for B. papendorfii UM 226 with different lowercase letters are significantly different (p < 0.05; ANOVA with Tukey’s post hoc test). ^A means for N. dimidiatum UM 880 are not significantly different (p > 0.05; ANOVA with Tukey’s post hoc test)

Fig. 10

Mycelial growth of B. papendorfii UM 226 and N. dimidiatum UM 880 in solution containing various concentration of urea. Results are expressed as mean ± standard error; n = 2. The means of B. papendorfii UM 226 and N. dimidiatum UM 880 were significantly different (p < 0.05; independent T-test) at 2–6% of urea. The means for both strains were not significantly different (p > 0.05) at 7% of urea