Draft genome sequence of the fungal pathogen Penicillium expansum (PPRI25879) isolated in South Africa

Abstract

Objectives

Penicillium expansum, a necrotrophic plant pathogen with a wide range of fruit hosts, is an important causal agent of blue mold rot. The fruit business suffers significant financial losses because of blue mold rot that occurs during fruit storage, transportation, and sale. The objective of this work was to generate a high-quality draft genome assembly of P. expansum, which will contribute to enhancing the management of blue mold, especially in stone and pome fruits, including grapes, by improving our understanding of the epidemiology of the pathogen and its interactions with the host.

Data description

Here, we describe the genome sequence of Penicillium expansum isolate PPRI25879, one of the most virulent strains isolated from grapes in South Africa. Sequencing reads from P. expansum produced approximately 3.5 Gb. The assembly generated a draft genome of size 32.1 Mb, consisting of 1648 contigs, with an N50 of 508 KB. Examination of the genome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the draft genome carries 97.9% of the 746 genes in the Eurotiomycetes_odb10 database. The draft genome sequence will allow improved genomic comparisons among the most important pathogens belonging to the Penicillium genus, with the aim of improving our knowledge of their plant-pathogen interactions, population biology, and control.

Objectives

Penicillium expansum is a filamentous phytopathogenic fungus belonging to the phylum Ascomycota, class Eurotiomycetes, and the genus Penicillium. Penicillium species are ubiquitous soil inhabitants that are typically found in decomposing vegetation on the orchard floor or soil [1]. P. expansum is the most common and aggressive among the Penicillium species [2]. This postharvest pathogen has significant economic importance, causing blue mold rot in a wide range of fruits, particularly pome and stone fruits, and produces carcinogenic mycotoxins that can be dangerous for animals and people [2,3,4]. Fruits are infected by this common wound parasite fungus through mechanical injury from rigorous handling during harvest and transportation, as well as by injuries caused by insects, birds, and adverse weather conditions, especially before harvest [5, 6], resulting in light brown discoloration or lesions on the skin as the infection spreads [7]. The infection is typically quick to expand across the fruit surface and inside the tissue, and the pathogen produces blue-green mold spore colonies that may appear on the surface of the fruit at advanced stages of decay [2], resulting in fruit frailty, and may also pose health risks to animal and human consumers [8]. The main source of inoculum is conidia, which can be found in the packinghouse in flume water, on bin surfaces, on fruit, and in the air [9].

The aim of this study was to assemble a high-quality draft genome of P. expansum using next-generation sequencing technology. The work presented here provides fundamental genomic information that could be valuable in enhancing the existing knowledge on the general knowledge of Penicillium biology and may contribute to the discovery of novel mechanisms of pathogenicity. The genome data also present an opportunity for further comparative genomic analysis of Penicilium species.

Data description

Strain PPRI25879 of P. expansum was isolated from grapes at the Agricultural Research Council (ARC) – Plant Health and Protection, Roodeplaat, Tshwane, South Africa. Symptomatic tissues were surface sterilized using 1% bleach and ethanol, and further plated on sugar-free agar and plant count agar + nutrient agar. The isolates were identified by morphological observations and PCR. The culture was stored as agar punches in sterile water and frozen at -80 °C. Prior to DNA sequencing, the culture was replated on ¼ potato dextrose agar and mycelia were scraped into a 2 ml microcentrifuge tube. DNA was extracted using the Quick-DNA miniprep Plus kit (Zymo Research, Irvine, CA, USA). Genomic DNA libraries were prepared using the TruSeq Nano DNA Library Prep Kit, and sequencing was performed using the Illumina MiSeq sequencing platform to produce paired-end sequences of 300 bp. The quality of the raw reads was assessed using FastQC v. 0.11.9, and low-quality bases and adaptor sequences were trimmed using Trim Galore v. 0.6.5. Filtered reads were de novo assembled using SPAdes v 3.15.4 assembler [10], and genome completeness was scored using BUSCO v 5.4.7 [11] against the Eurotiomycetes _odb10 database. The genome assembly quality was assessed using Quast v 5.2.0 [12]. The assembly statistics, raw sequence data and genome assembly data are listed in Table 1, Data file 1 [13], Data set 1 and Data set 2 [14, 15]. A draft genome assembly of 32 116 299 bp of nucleotides and 47.68% GC content were assembled. This draft genome assembly has a sequencing depth of 87.4X with total of 1648 contigs (> 200 bp).

Overall, genome completeness assessment on the draft assembled genome quality showed that a 97.9% complete (742 of complete and single copy gene found / 746 complete BUSCO genes of Eurotiomycetes _odb10).

Table 1 Overview of data files/data sets

Limitations

The genome assembly presented in this study was obtained from a single strain of P. expansum and has not been annotated.