Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom

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.

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

“…A total of 38.48 Mb of reads were assembled into eight contigs, with a contig N50 of 4.76 Mb, an N90 of 4.40 Mb, and a maximum span of 7.02 Mb. The size of the assembled genome was smaller than previously reported for C. protrusum (39.09 Mb) [17] and M. perniciosa (44.00 Mb) [18], but larger than other species within the Hypocreaceae, including T. longibrachiatum (32.24 Mb) [25], T. reesei (33.39 Mb) [26], and Escovopsis weberi (27.20 Mb) [27]. The guanine-cytosine (GC) content of the C. dendroides genome was 48.2%.…”

“…However, sequenced genomes in this genus (Hypomyces/Cladobotryum) are scarce. To date, only the genomes of C. protrusum and H. perniciosa (the sexual morph of M. perniciosa) have been released [17,18]. C. protrusum is the only species of Cladobotryum for which a genome is available [17].…”

“…To date, only the genomes of C. protrusum and H. perniciosa (the sexual morph of M. perniciosa) have been released [17,18]. C. protrusum is the only species of Cladobotryum for which a genome is available [17]. It is imperative to obtain additional genome data in order to rapidly identify pathogenic genes and characterize fungi-fungi interactions in the Cladobotryum.…”

“…Associated advances have improved the identification of pathogenicity-related genes and revealed the molecular mechanisms underlying pathogenesis. To date, several pathogenic genomes have been sequenced using Pacific Biosciences (PacBio) Sequel or the RSII platform [17,18,20]. With these available genomic sequences, it is possible to determine the evolutionary relationships among fungi [21][22][23][24], as well as to explore the evolution of nutritional mode.…”

“…With these available genomic sequences, it is possible to determine the evolutionary relationships among fungi [21][22][23][24], as well as to explore the evolution of nutritional mode. In addition, numerous gene clusters associated with pathogenicity have been identified, including secretory proteins, membrane transport proteins, pathogen-host interaction (PHI) genes, fungal virulence factors, and fungal G proteins [17,18]. In addition, some expanded or contracted orthologous, species-specific genes and positive selective genes, including protein kinases, serine peptidases, cell-wall proteins, carbohydrate-active enzymes (CAZymes), secondary metabolites (SMs), and P450, were shown to be involved in biological control activity, pathogenesis, and mycoparasitism [21,22,24].…”