Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism

Abstract

Cladobotryum dendroides, which causes cobweb disease in edible mushrooms, is one of the major fungal pathogens. Our previous studies focused on the genetic and morphological characterization of this fungus, as well as its pathogenicity and the identification of appropriate fungicides. However, little is known about the genome characters, pathogenic genes, and molecular pathogenic mechanisms of C. dendroides. Herein, we reported a high-quality de novo genomic sequence of C. dendroides and compared it with closely-related fungi. The assembled C. dendroides genome was 36.69 Mb, consisting of eight contigs, with an N50 of 4.76 Mb. This genome was similar in size to that of C. protrusum, and shared highly conserved syntenic blocks and a few inversions with C. protrusum. Phylogenetic analysis revealed that, within the Hypocreaceae, Cladobotryum was closer to Mycogone than to Trichoderma, which is consistent with phenotypic evidence. A significant number of the predicted expanded gene families were strongly associated with pathogenicity, virulence, and adaptation. Our findings will be instrumental for the understanding of fungi–fungi interactions, and for exploring efficient management strategies to control cobweb disease.

Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms

“…Reciprocal BLASTp searches were conducted ( e -value ≤ 1 × 10 −7 ) with protein sequences from the representative species of Eurotiomycetes (four Eurotiales species: Paecilomyces variotii [ 35 ], Penicillium chrysogenum [ 36 ], Aspergillus nidulans [ 37 ], and A. niger [ 38 ]) and Sordariomycetes (Hypocreales species: Metarhizium robertsii [ 39 ], T. atroviride [ 40 ], T. harzianum [ 41 ], Trichoderma reesei [ 42 ], T. virens [ 43 ], C. dendroides [ 16 ], C. protrusum [ 13 ], H. perniciosus [ 15 ], Cordyceps militaris [ 44 ], Fusarium graminearum [ 45 ], and Niesslia exilis ( ), Ophiocordyceps unilateralis [ 46 ], Stachybotrys chartarum [ 47 ], and one Sordariales species: Neurospora crassa [ 48 ]) were included to obtain single-copy ortholog sequences. Schizosaccharomyces pombe [ 49 ] in Schizosaccharomycetes was used as an outgroup for this analysis.…”

“…With the rapid development of sequencing technologies, an increasing number of fungal genomes have become available [ 12 , 13 , 14 ]. Phylogenetic analysis of the single-copy orthologous genes has been widely used for evolutionary studies and provides improved resolution for elucidating the phylogenetic relationships of organisms compared to the use of sequences from one or a few genes [ 13 , 15 , 16 , 17 ]. Due to the lack of P. penicillatus genomic resources, a comprehensive phylogenetic analysis based on single-copy orthologous genes is not available.…”

“…Though not known from P. penicillatus , lysis of the host cell wall is a common mechanism of mycoparasitism [ 18 ]. Many mycoparasitic fungi have been identified in Hypocreaceae, including Cladobotryum dendroides and Cladobotryum protrusum , which can cause cobweb disease, as well as Hypomyces perniciosus , the causative agent of wet bubble disease [ 13 , 15 , 16 ]. In particular, Trichoderma spp.…”

Control of Fungal Diseases in Mushroom Crops while Dealing with Fungicide Resistance: A Review

“…Cobweb is a globally widespread pathology whose causative agent corresponds with several Ascomycota species described as harmful in different mushroom-producing countries and all belonging to the genera Cladobotryum spp. Among them, C. dendroides [ 26 ], C . mycophilum [ 79 ], C. protrusum [ 25 ], or C. varium [ 80 ] have been described as parasites of cultivated mushrooms but also infecting mushrooms in the wild [ 81 ].…”

“…Likewise, mechanisms of host–microorganism interaction are still mostly unknown. However, different genomic resources, including the release of host [ 22 ] and some mycoparasite genomes [ 23 , 24 , 25 , 26 ], have been disclosed within recent years. The knowledge available can, for instance, serve as a tool for mapping quantitative trait loci (QTL) of mycoparasite-resistant genes in the mushroom host through data mining [ 27 , 28 ].…”