We report the assembly and annotation of 10 different black yeast genomes from microbiome metagenomic data derived from biofouled plastic fabrics. The draft genomes are estimated to be 9 to 33.2 Mb, with 96 to 1,257 contigs and G+C contents of 43.9% to 57.4%, and they harbor multiple genes for hydrocarbon adaptation and degradation.
ABSTRACT
We report the assembly and annotation of 10 different black yeast genomes from microbiome metagenomic data derived from biofouled plastic fabrics. The draft genomes are estimated to be 9 to 33.2 Mb, with 357 to 5,108 contigs and G+C contents of 43.9% to 57.4%, and they harbor multiple genes for hydrocarbon adaptation and degradation.
ANNOUNCEMENT
Black yeast is a diverse group of fungi, belonging to the Chaetothyriomycetidae and Dothideomycetidae subclasses of ascomycetes, with the ability to degrade hydrocarbons and plasticizers (1–3). In this study, the metagenome-assembled genomes (MAGs) of 10 black yeast species were assembled and annotated from a shotgun metagenomic library of microbiomes associated with biofouled plastic fabric materials (4).
As described by Radwan et al., total genomic DNA was extracted from plasticized fabrics exposed to the Panama jungle for 14 months, and the DNA libraries were sequenced using a shotgun metagenomic approach (4). To maximize DNA extraction efficiency, fabrics were cut into 0.5-cm2 pieces, and DNA was extracted using the DNeasy UltraClean kit (catalogue number 12224-250; Qiagen) (4). DNA libraries were constructed using the PrepX DNA library kit and the Apollo 324 next-generation sequencing (NGS) automatic library preparation system (WaferGen, Fremont, CA). The TruSeq paired-end DNA libraries were sequenced using an Illumina HiSeq 2000 system, generating 161,537,275,209 bp of raw reads of 100-bp length (4). Trimmomatic v0.36 with the RepBase-20170 library (5) was used for quality control, removing raw reads shorter than 50 bp and those with an average quality score below 15. Multiple bioinformatics programs (6) were used with default parameters except where otherwise noted. After sorting of paired-end reads for compatibility and normalization using BBtools (https://jgi.doe.gov/data-and-tools/bbtools), reads were assembled by the MEGAHIT assembler (7) with options of minimum contig length of 200 bp and meta-sensitive. Fasta contigs produced by MEGAHIT with coverage and abundance files for each fabric sample were used by MaxBin v2.7.7 (8) to bin individual genomes with options of minimum contig length of 2000 and depth of 2.
DNA sequences of 10 different black yeast genomes were selected for assembly improvement and sequence gap filling using SSPACE v3.0 (9) and GapFiller v1.10 (10), respectively (Table 1). After masking of the repetitive sequences with RepeatMasker (11), the genes of each genome were predicted by AUGUSTUS v2.5.5 (12) with an option set for Yarrowia lipolytica. CEGMA (13) was used to calculate genome completeness, which ranged from 13.64% for Hortaea werneckii to 94.00% for Exophiala oligosperma. According to the MAG completeness criteria (14), two MAGs were high quality, two were medium quality, and six were low-quality drafts reflecting partial genomes. ABySS v2.0.2 (15) calculated genome sizes ranging from 9 to 33.2 Mb, with L50 values of 22 to 1,258 contigs and G+C contents of 43.9% to 57.4% (Table 1). HMMER v3.3 (16) with E values of 1e−3 was used to search the Pfam database for functional annotation of proteins involved in hydrocarbon degradation (i.e., cytochrome P450 and aromatic ring-opening dioxygenases), hydrolases (esterases and lipases), and efflux pumps potentially associated with hydrocarbon resistance (Table 1). The number of protein-coding genes identified for each pathway depended on the assembled genome completeness and species. For example, Exophiala oligosperma, with a genome completeness of 94.00%, contained the highest number of proteins belonging to different pathways, while Hortaea werneckii, with only 13.64% completeness, contained the lowest number of proteins. The results of this study support the ability of black yeasts such as Exophiala oligosperma and Cyphellophora europaea to degrade hydrocarbons (17, 18) and plasticizers (1, 2).
TABLE 1.
Accession numbers, general statistics of black yeast MAGs, and numbers of genes involved in hydrocarbon degradation, polymer hydrolysis, and efflux pumps for each genomea
| Codeb | Genome | GenBank accession no. | Size (bp) | No. of contigs | L50 (contigs) | N50 (bp) | G+C content (%) | Completeness (%)c | No. of degradation genes | No. of hydrolase genes | No. of MFSd | No. of ABCe |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A04 | Exophiala oligosperma | JADCRK000000000 | 33,192,209 | 357 | 22 | 451,697 | 51.6 | 94.00 | 137 | 6 | 143 | 85 |
| B02 | Rhinocladiella mackenziei | JADCRN000000000 | 26,458,337 | 925 | 101 | 73,418 | 43.9 | 93.95 | 19 | 0 | 50 | 16 |
| B03 | Baudoinia panamericana | JADCRE000000000 | 27,253,305 | 5,108 | 1,198 | 6,330 | 49.7 | 68.55 | 112 | 4 | 125 | 65 |
| B04 | Cyphellophora europaea | JADCRG000000000 | 18,212,429 | 4,098 | 1,132 | 4,855 | 54.4 | 55.65 | 77 | 3 | 216 | 63 |
| B06 | Exophiala sp. | JADCRL000000000 | 20,651,700 | 4,626 | 1,258 | 4,953 | 45.8 | 47.58 | 26 | 0 | 47 | 20 |
| C02 | Cyphellophora europaea | JADCRH000000000 | 18,567,089 | 4,594 | 1,232 | 4,116 | 56.9 | 42.74 | 74 | 3 | 178 | 31 |
| A11 | Baudoinia panamericana | JADCRF000000000 | 13,998,733 | 3,358 | 935 | 4,505 | 49.9 | 39.52 | 28 | 3 | 53 | 13 |
| F22 | Cyphellophora europaea | JADCRI000000000 | 11,716,283 | 3,003 | 806 | 4,045 | 55.3 | 24.19 | 23 | 3 | 131 | 67 |
| B07 | Cyphellophora europaea | JADCRJ000000000 | 9,001,416 | 2,896 | 1,036 | 3,049 | 57.4 | 18.95 | 80 | 4 | 166 | 14 |
| A17 | Hortaea werneckii | JADCRM000000000 | 9,816,071 | 2,164 | 625 | 5,040 | 52.6 | 13.64 | 1 | 0 | 1 | 11 |
The Pfam database with E values of 1e−3 was used for functional annotation. High-quality (A04 and B02), medium-quality (B03 and B04), and low-quality (C02, A11, F22, B06, B07, and A17) draft genomes are shown. The taxonomic identity of each species was determined using Kaiju (19).
A04, A11, and A17 were derived from physical biosample A (BioSample accession number SAMN16111753; SRA accession number SRS7586490). B02, B03, B04, B06, and B07 were derived from physical biosample B (BioSample accession number SAMN16111857; SRA accession number SRS7586491). C02 was derived from physical biosample C (BioSample accession number SAMN16111912; SRA accession number SRS7586492). F22 was derived from physical biosample F (BioSample accession number SAMN16112156; SRA accession number SRS7586495).
Genome completeness was estimated with CEGMA software (13).
MFS, major facilitator superfamily efflux pumps.
ABC, ABC transporters.
Data availability.
The raw sequence reads and MAGs were deposited in DDBJ/ENA/GenBank under BioProject accession number PRJNA656291 with BioSample accession numbers SAMN15776667 to SAMN15776676 and SRA accession numbers SRX9364069 to SRX9364074. Individual accession numbers for MAGs are provided in Table 1. HMMER results can be retrieved from Mendeley Data at https://data.mendeley.com/datasets/kh6x88k83y/1.
ACKNOWLEDGMENTS
This material is based on research sponsored by the Air Force Research Laboratory, Aerospace Systems Directorate (AFRL/RQTF), under agreement FA8650-16-2-2605.
The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of AFRL/RQTF or the U.S. Government.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The raw sequence reads and MAGs were deposited in DDBJ/ENA/GenBank under BioProject accession number PRJNA656291 with BioSample accession numbers SAMN15776667 to SAMN15776676 and SRA accession numbers SRX9364069 to SRX9364074. Individual accession numbers for MAGs are provided in Table 1. HMMER results can be retrieved from Mendeley Data at https://data.mendeley.com/datasets/kh6x88k83y/1.