Draft Genome Sequence of the Dimorphic Fungus Sporothrix pallida, a Nonpathogenic Species Belonging to Sporothrix, a Genus Containing Agents of Human and Feline Sporotrichosis

Abstract

Sporothrix pallida is considered to be a mostly avirulent environmental fungus, phylogenetically closely related to the well-known pathogen Sporothrix schenckii. Here, we present the first assembly of its genome, which provides a valuable resource for future comparative genomic studies between nonpathogenic and pathogenic Sporothrix spp.

GENOME ANNOUNCEMENT

In recent years, the fungal genus Sporothrix has aroused considerable interest because of the worldwide emergence of some pathogenic species that cause sporotrichosis, a mycosis that affects humans and other mammals (1, 2). The best-known species of the group is Sporothrix schenckii, a thermodimorphic fungus with a worldwide distribution, even though the infection that it causes is more common in tropical and subtropical regions (2, 3). However, recent studies (4–6) have shown that the global S. schenckii population is a complex of cryptic species comprising four different closely related taxa with diverse degrees of virulence and pathogenicity (7), while occasional opportunists are found elsewhere in the genus.

Sporothrix pallida (formerly Sporothrix albicans) is considered an avirulent environmental species of the genus Sporothrix, and although one case of human keratitis has recently been reported (8), it was found to be nonpathogenic for mice and represents certainly a less versatile pathogen when compared to other members of the S. schenckii complex (7).

One of the main difficulties in the study of these fungi is the lack of exhaustive genomic information, which limits our understanding of their basic biology, including their interactions with the mammalian host. Recently, the genome sequences of S. schenckii and S. brasiliensis have been released (9, 10), and we can now add the S. pallida genome in order to provide essential data for future comparative genomic studies among highly pathogenic species and closely related species with reduced or absent virulence.

The genome of S. pallida strain SPA8 (5, 11) was sequenced using Ion Torrent (PGM) (318-chip) and Illumina HiSeq 2000 technologies. For sequencing, we constructed four different DNA libraries: one library was generated for single-read sequencing on an Ion PGM machine, while three libraries, with different insert sizes (200 bp, 500 bp, and 6 kb), were used for paired-end Illumina sequencing. Before assembly, raw reads were processed to remove adapters and polyclonal sequences and subsequently filtered and trimmed using FASTX-Toolkit version 0.0.14 (http://hannonlab.cshl.edu/fastx_toolkit) to remove sequences with low Phred-scores (cutoff quality score: ≥20). The final data set used for assembly contained 4,113,066 quality-controlled Ion PGM reads and 21,915,508, 16,647,776, and 16,763,936 clean reads obtained from 200-bp, 500-bp, and 6-kb Illumina libraries, respectively.

The S. pallida genome was assembled de novo using MIRA version 4.0.2 (12) and SPAdes (13). The assembled genome resulted in 432 contigs (>200 bp; largest contig, 860,569 bp; N₅₀, 224,849 bp) with a total consensus length of 37,819,765 bp (G+C content: 52.8%) at 50× coverage. A total of 11,356 protein-encoding genes were predicted ab initio by AUGUSTUS (14), and 151 putative tRNA genes were found by tRNAscan-SE (15). The entire mitochondrial genome, identified using GRAbB (16), was contained in a single contig (Contig_215) of our assembly and was found to be circular.

Hence, the genome of the nonpathogenic S. pallida genome proves to be approximately 5 Mb larger than the genomes of its human pathogenic relatives (9, 10). Further genomic analysis will be of great help to understand the genetics and evolution of pathogenic and nonpathogenic Sporothrix spp.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JNEX00000000. The version described in this paper is the second version, JNEX02000000.

Funding Statement

This work, including the efforts of Carla Lo Passo, was funded in part by University of Messina (PRA2008/09-ORME097YB2). This work was also supported in part by a grant (no. 81371746) from the National Nature Foundation of China to Huaiqiu Huang.