Abstract
Cladobotryum protrusum is one of the mycoparasites that cause cobweb disease on cultivated edible mushrooms. However, the molecular mechanisms of evolution and pathogenesis of C. protrusum on mushrooms are largely unknown. Here, we report a high-quality genome sequence of C. protrusum using the single-molecule, real-time sequencing platform of PacBio and perform a comparative analysis with closely related fungi in the family Hypocreaceae. The C. protrusum genome, the first complete genome to be sequenced in the genus Cladobotryum, is 39.09 Mb long, with an N50 of 4.97 Mb, encoding 11,003 proteins. The phylogenomic analysis confirmed its inclusion in Hypocreaceae, with its evolutionary divergence time estimated to be ~170.1 million years ago. The genome encodes a large and diverse set of genes involved in secreted peptidases, carbohydrate-active enzymes, cytochrome P450 enzymes, pathogen–host interactions, mycotoxins, and pigments. Moreover, C. protrusum harbors arrays of genes with the potential to produce bioactive secondary metabolites and stress response-related proteins that are significant for adaptation to hostile environments. Knowledge of the genome will foster a better understanding of the biology of C. protrusum and mycoparasitism in general, as well as help with the development of effective disease control strategies to minimize economic losses from cobweb disease in cultivated edible mushrooms.
Highlights
As the commercial cultivation of edible mushrooms continuously expands worldwide, the occurrence of diseases caused by fungal pathogens is increasing, seriously affecting mushroom quality and yield [1]
Core Eukaryotic Genes Mapping Approach (CEGMA) [19] analysis revealed that 97.58% of the core eukaryotic genes were contained in the assembly (242 out of 248 core eukaryotic genes), while the BUSCO [21] assessment results showed that 99.7% (289 out of 290 genes) of genes were covered by the assembled genome containing 99%, 0.7%, and 0.3% of complete, duplicated, and missing BUSCOs [21], respectively
We sequenced the genome of C. protrusum, a pathogen that causes cobweb disease on cultivated edible mushrooms, using the PacBio sequencing platform
Summary
As the commercial cultivation of edible mushrooms continuously expands worldwide, the occurrence of diseases caused by fungal pathogens is increasing, seriously affecting mushroom quality and yield [1]. Ascomycota, class Sordariomycetes, order Hypocreales, and family Hypocreaceae, are causal agents of cobweb disease on a number of economically important mushroom crops, such as Agaricus bisporus, Flammulina velutipes, Pleurotus ostreatus, P. eryngii, Hypsizygus marmoreus, and Ganoderma lucidum [3,4,5,6,7,8]. The species C. dendroides, C. mycophilum, C. protrusum, and C. varium are pathogens that frequently cause cobweb disease in commercial mushroom farms. The characteristic symptom of cobweb disease is the abundance of coarse mycelium [9], which covers the affected mushrooms with numerous spores and spreads rapidly in commercial growth rooms, leading to serious economic losses worldwide [5,10,11]. Among the Cladobotryum genus, C. protrusum is an important member, as it causes cobweb disease on edible mushrooms, such as Coprinus comatus, Agaricus bisporus, and P. ostreatus, and has the widest distribution [12,13].
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