Genome sequences of three plastic-debris-inhabiting fungi isolated from New Zealand waste and recycling management plants

TL;DR

This paper presents the genome sequences of three fungi found on plastic debris in New Zealand recycling and waste facilities.

Contribution

The study provides new genomic data for understudied Cladosporium and Epicoccum fungi species.

Findings

Draft genomes of three fungi were sequenced and deposited in GenBank.

The fungi were isolated from plastic debris in waste and recycling facilities in New Zealand.

These genomes add to the limited genomic resources for Dothideomycetes fungi.

Abstract

Cladosporium and Epicoccum are cosmopolitan fungi of the class Dothideomycetes with few cultured and genomic representatives. Here, we report draft reference genome sequences of Epicoccum sp. F181 (GenBank accession number JAJSLS01), Cladosporium sp. F165 (JAJSLR01), and F190 (JAJSLT01) isolated from recycling and waste management facilities in New Zealand.

Tables

TABLE 1. Genomic features and assembly statistics of representative Epicoccum sp. and Cladosporium sp. genomes

Metadata
Assigned taxonomy	Epicoccum sp.	Cladosporium sp.
Strain identifier	F181	F165	F190
Isolate name alias	Lan181-CD2	Lan165-M2b	Rec190-CD2b
NCBI Taxonomy ID	2904842	2904843	2904841
Isolation source	Marton Landfill		Awapuni Resource Recovery Park
Isolation Country	New Zealand
Genome project information
GenBank accession numbers	JAJSLS01	JAJSLR01	JAJSLT01
BioSample ID	SAMN24012772	SAMN24012771	SAMN24012773
Assembly ID (GCA)	GCA_037042865	GCA_037042895	GCA_037042825
PacBio data
SRA accession|Run IDs	SRX15217855|SRR19151143	SRX15217856|SRR19151142	SRX15217854|SRR19151144
Total read length (bp)	4,683,302,991	4,052,731,060	4,645,967,316
No. of subreads	353,079	292,837	352,112
N50 read length (bp)	17,586	17,706	17,460
Illumina data
SRA accession|Run IDs	SRX13451535|SRR17273850	SRX13451534|SRR17273851	SRX13451536| SRR17273849
Total read length (bp)	1,657,148,644	1,928,529,818	1,925,560,242
No. of filtered reads (bp)	1,356,558,704	1,651,738,291	1,562,163,222
Genome assembly statistics
Assembly size (bp)	36,126,079	34,560,626	33,867,326
Genome coverage (×)	130	117	137
G + C content (%)	51.6	52.5	52.6
DNA contigs	40	40	34
Contig N50 (bp)	1,412,226	2,068,171	1,945,840
Contig L50	9	8	8
BUSCO C| M (%)a	99.3|0.7	99.7|0.3	99.6|0.4

Full text

ANNOUNCEMENT

Members belonging to the Dothideomycetes classes of ascomycetes are diverse, with biofouling and degradative abilities of synthetic plastic polymer materials (1–4). In 2018, Epicoccum sp. F181 and Cladosporium sp. F165 were originally isolated from recycled plastic trays collected from the Awapuni Resource Recovery Park (Palmerston North, New Zealand), whereas Cladosporium sp. F190 was isolated from the Marton Landfill (Marton, New Zealand). Fungi were cultured for 5 days into 10 mL minimal salt medium (MSM) at 25°C (5) supplemented with glucose and low-density polyethylene (LDPE). The presented draft reference genomes are valuable resources for future studies investigating genome evolution of potentially novel fungal species able to colonize plastic surfaces.

For genomic sequencing of each isolate, cryostocks were revived and mycelium was grown for 5 days in 80 mL potato dextrose broth (Sigma-Aldrich) at 25°C and washed with phosphate-buffered saline at 5,000 × g for 5 min. Genomic DNA was extracted by grinding in liquid nitrogen and extracting with Zymo Fungal/Bacteria DNA Miniprep Kit (Zymo Research) and was purified using Zymo Clean & Concentrator kit (Zymo Research), following the manufacturer's instructions. DNA quantity, quality, and integrity were assessed using the High Sensitivity DNA LabChip Kit on the Bioanalyzer 2100 (Agilent Technologies). Each fungal strain was identified by PCR amplification of the Internal Transcribed Spacer (ITS) region using ITS4 and ITS5 primers and amplification protocol (6), sequenced on an ABI 3730 DNA system (Applied Biosystems), and alignment to the NCBI refseq ITS database using BLAST v2.9.0 (7). Strain identities were confirmed (99% identity) for Epicoccum sp. F181 (GenBank accession number PP896550) as Epicoccum endophyticum (GenBank accession number NR_172436), Cladosporium sp. F165 (GenBank accession number PP896549) as Cladosporium chasmanthicola (NR_152307), and Cladosporium sp. F190 (GenBank accession number PP896551) as Cladosporium pseudocladosporioides (NR_152296).

For each isolate, approximately 12 µg of genomic DNA was sequenced using a combination of Illumina and PacBio Single Molecule Real Time (SMRT) technologies (Table 1). For Illumina, 250 bp paired-end reads were sequenced using the Nextera XT DNA library prep kit v2 (Illumina) on the MiSeq platform. The SolexaQA++ software v3.1.7.3 (8) was used to check the quality of the raw reads and perform read trimming with standard parameters. Prior to library preparation for PacBio sequencing, Covaris g-TUBEs (Covaris) were used to fragment the genomic DNA, AMPure PacBio beads (PacBio) for purification, and BluePippin system (Sage Science) to select for fragment size of >20 kb. DNA fragments were end-repaired to construct SMRTbell DNA template libraries with a Bioanalyzer used to assess quality and fragment size estimation. Long-read libraries were prepared using the SMRTbell DNA CLR template prep kit v2.0 (PacBio) and sequenced on three SMRT cells using a Sequel II v8.0 system in continuous long read (CLR) mode with SMRT Link v11.1 used for data acquisition. Reads were preprocessed using Fastp v0.21.0 with a > Q30 threshold (9), followed by a hybrid de novo assembly correcting the refined PacBio reads with Illumina trimmed data performed with Canu v2.2 (10). We polished the assembly with one round of PILON v1.24 (11). Assembly quality and completeness were evaluated by BUSCO v5.4.4 (12) using the lineage “fungi_odb10 database”. Default parameters were used for all software unless otherwise specified. The sequencing data metrics and genome features are summarized in Table 1.