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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39088317
mra00266-24
10.1128/mra.00266-24
mra.00266-24
Genome Sequences
applied-and-industrial-microbiologyApplied and Industrial MicrobiologyGenome sequences of three plastic-debris-inhabiting fungi isolated from New Zealand waste and recycling management plants
https://orcid.org/0000-0002-2101-2452
Palevich Nikola 1 Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Project administration Resources Software Supervision Validation Visualization Writing – original draft Writing – review and editing nik.palevich@agresearch.co.nz

https://orcid.org/0000-0001-9946-2720
Wu Shuyan 2 Formal analysis Funding acquisition Investigation Project administration Validation
https://orcid.org/0000-0001-9371-9978
Li Yang 1 3 Conceptualization Formal analysis Funding acquisition Investigation Methodology Project administration Resources Supervision Writing – review and editing Validation Writing – original draft
https://orcid.org/0009-0003-0077-6343
Palevich Faith P. 2 Formal analysis Investigation Methodology Validation Resources
https://orcid.org/0000-0001-8898-8276
Maclean Paul H. 1 Investigation Software Validation Formal analysis Methodology Resources Supervision Writing – original draft
https://orcid.org/0000-0002-0940-1404
Singh Sidhu Jaspreet 1 Investigation
Subharat Pornchanok 2 Investigation
https://orcid.org/0000-0002-3484-8937
Jauregui Ruy 4 Investigation
Müller Jana L. 5 Investigation Methodology Resources
https://orcid.org/0000-0002-0464-8811
Reilly Kerri 1 Project administration
https://orcid.org/0000-0002-4603-9117
Mills John 2 Project administration
https://orcid.org/0000-0002-6443-8760
Attwood Graeme T. 1 Investigation Project administration Supervision Conceptualization
https://orcid.org/0000-0002-3980-4108
Brightwell Gale 2 Project administration Supervision
1 AgResearch Ltd., Grasslands Research Centre , Palmerston North, New Zealand
2 AgResearch Ltd., Hopkirk Research Institute , Palmerston North, New Zealand
3 Institute of Agricultural Sciences, ETH Zurich (Eidgenössische Technische Hochschule Zürich) , Zurich, Switzerland
4 Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries , Wallaceville, New Zealand
5 Kantonale Veterinäramt Zürich (Zürich Cantonal Veterinary Office) , Zürich, Switzerland
Editor Bruno Vincent Michael University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Nikola Palevich, nik.palevich@agresearch.co.nz
The authors declare no conflict of interest.

9 2024
01 8 2024
01 8 2024
13 9 e00266-2417 3 2024
16 7 2024
Copyright © 2024 Palevich et al.
2024
Palevich et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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.

KEYWORDS

Cladosporium
Epicoccum
fungi
plastic waste
genome
New Zealand Ministry of Business, Innovation and Employment - Strategic Science Investment Fund 12575 Li Yang New Zealand Ministry of Business, Innovation and Employment - Strategic Science Investment Fund PRJ0126336 Mills John Brightwell Gale New Zealand Ministry of Business, Innovation and Employment - Strategic Science Investment Fund PRJ0331443 Wu Shuyan Mills John New Zealand Ministry of Business, Innovation and Employment - Strategic Science Investment Fund A25768 Brightwell Gale cover-dateSeptember 2024
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pmcANNOUNCEMENT

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.

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	
a C and M refer to complete and missing BUSCO fungal genes (n = 758).

ACKNOWLEDGMENTS

This work was supported by the New Zealand Ministry of Business, Innovation and Employment (MBIE) through the Strategic Science Investment Fund (SSIF), which funded the initial sampling and isolation work (12575) but also the presented research (PRJ0126336, PRJ0331443, and A25768). We acknowledge Xiao Xiao Lin (Massey Genome Service, New Zealand) for assistance with the DNA sequencing services. We thank Ron Ronimus and Vince Carbone for reviewing an earlier version of the manuscript and their helpful feedback.

DATA AVAILABILITY

The whole-genome sequence data and raw sequences are available at NCBI under the BioProject accession number PRJNA788622. Detailed information regarding GenBank, BioSample, Assembly, and Sequence Read Archive (SRA) accession number identifiers can be found in Table 1.
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