Draft Genome Sequence of Fonsecaea nubica Strain CBS 269.64, Causative Agent of Human Chromoblastomycosis

Abstract

On the basis of multilocus phylogenetic data, Fonsecaea nubica was described in 2010 as a molecular sibling of F. monophora, an established agent of the human skin disease chomoblastomycosis in tropical zones. Genome analysis of these pathogens is mandatory to identify genes involved in the interaction with host and virulence.

GENOME ANNOUNCEMENT

The genus Fonsecaea comprises anamorph members in the Chaetothyriales, an ascomycete order of black yeasts and filamentous relatives covering numerous opportunistic pathogens on humans (1–3). Fonsecaea is one of the prevalent genera of etiologic agents of chromoblastomycosis (4, 5), a chronic, cutaneous, and subcutaneous infection characterized by slowly expanding, polymorphic skin lesions with muriform cells in tissue, provoking a granulomatous immune response (6, 7). The disease occurs preferentially in humans, although some cases have been reported in other mammals (8–10). Several Fonsecaea species are involved as etiologic agents of the disease, i.e., F. pedrosoi, F. monophora, F. nubica, and F. pugnacius, each with different virulence potentials (6, 11). F. nubica was first described in 2010 with type strain CBS 269.64, isolated from a human patient with chromoblastomycosis in west Cameroon (6, 12). Genome analysis of the pathogenic fungus F. nubica is needed to identify genes involved in the interaction with host cells and molecular mechanisms in response to cytotoxic agents (13).

Strain F. nubica CBS 269.64 was grown in Sabouraud’s broth, with shaking at 150 rpm at 28°C for 7 days and DNA was extracted by the cetyltrimethylammonium bromide (CTAB) method with phenol-chloroform/isoamyl alcohol. Total DNA was purified with the microbial DNA UltraClean kit. DNA of F. nubica was used for library construction using the Ion Plus Fragment library kit (Thermo, FisherScientific) and Nextera XT (Illumina) following the manufacturer’s instructions. The libraries were sequenced on an Ion Proton (Thermo, FisherScientific) for single-end reads and in Miseq (Illumina) for paired-end reads. The quality of the reads was assessed by means of FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). The reads were assembled de novo using SPADES v3.6.2 (14). The draft genome comprised 258 contigs and the genome size was 33.7 Mb, with a G+C content of 52.46%. Protein-coding genes were predicted with GeneMark-ES (15). Gap closure was performed with FGAP software (16). Annotation for 11,681 predicted genes were assigned based on similarity searches against the nr database using RAFTS3 (17) and InterProScan (18) comparisons. The genome contained 36 tRNAs identified using ARAGORN (19).

Information about the genome sequence of this black yeast might provide a better understanding of the basic mechanisms of adaptation to requirements of the environmental habitat, and of pathogenicity and virulence.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession number LVCJ00000000. The version described in this paper is version LVCJ01000000.