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Summary of the P. penicillatus CCMJ2836 genome.
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Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still...
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Context 1
... genome of P. penicillatus CCMJ2836 strain was sequenced on the PacBio SMRT Sequel platform using two SMRT cells. A total of 4,266 Mb clean data (~105 × coverage) was generated (Table S1). The de novo assembly of the P. penicillatus genome was ~40.20 Mb, consisting of 52 scaffolds with 2.60 Mb in N50 value and 44.70% in guanine-cytosine (GC) content (Table 1). ...Context 2
... total of 4,266 Mb clean data (~105 × coverage) was generated (Table S1). The de novo assembly of the P. penicillatus genome was ~40.20 Mb, consisting of 52 scaffolds with 2.60 Mb in N50 value and 44.70% in guanine-cytosine (GC) content (Table 1). The completeness of the P. penicillatus genome was assessed through the CEGMA and BUSCOs analyses, with completeness scores of 95.56% and 97.20%, respectively. ...Context 3
... Materials: The following are available online at http://www.mdpi.com/2076-0817/9/10/834/s1, Text S1: Annotation of the genome of P. penicillatus, Table S1: CEGMA analysis on the completion of the P. penicillatus genome, Table S2: Functional annotation of the genes in the P. penicillatus genome against several databases, Table S3: The statistics of the repeat sequences in the P. penicillatus genome, Table S4: Annotation of tRNA, rRNA, miRNA, and snRNA in the P. penicillatus genome. ...Similar publications
The oyster mushroom Pleurotus ostreatus is a basidiomycete commonly found in the rotten wood and it is one of the most cultivated edible mushrooms globally. Pleurotus ostreatus is also a carnivorous fungus, which can paralyze and kill nematodes within minutes. However, the molecular mechanisms of the predator–prey interactions between P. ostreatus...
Citations
... The continuous cropping caused an imbalance of microbial populations in the soil matrix, especially by enriching harmful microorganisms (including bacteria and fungi), which harmed the growth of morel and the development of ascomata [39]. pointed out that the inhibition of the mycelial growth of M. sextelata was caused by a soluble compound rather than volatile compounds secreted by Paecilomyces penicillatus, based on confrontation tests between P. penicillatus and M. sextelata, and analyzed the characteristics of the P. penicillatus fungal cell wall-degrading enzyme system and the antifungal, antibacterial, and insecticidal activity of secondary metabolite gene clusters at the genomic level [79]. 1-octen-3-ol is a volatile compound of mushrooms with broad-spectrum antifungal activity. ...
Morels are one of the most highly prized edible and medicinal mushrooms worldwide. Therefore, historically, there has been a large international interest in their cultivation. Numerous ecological, physiological, genetic, taxonomic, and mycochemical studies have been previously developed. At the beginning of this century, China finally achieved artificial cultivation and started a high-scale commercial development in 2012. Due to its international interest, its cultivation scale and area expanded rapidly in this country. However, along with the massive industrial scale, a number of challenges, including the maintenance of steady economic profits, arise. In order to contribute to the solution of these challenges, formal research studying selection, species recognition, strain aging, mating type structure, life cycle, nutrient metabolism, growth and development, and multi-omics has recently been boosted. This paper focuses on discussing current morel cultivation technologies, the industrial status of cultivation in China, and the relevance of basic biological research, including, e.g., the study of strain characteristics, species breeding, mating type structure, and microbial interactions. The main challenges related to the morel cultivation industry on a large scale are also analyzed. It is expected that this review will promote a steady global development of the morel industry based on permanent and robust basic scientific knowledge.
... In recent years, with the continuous expansion of morel cultivation in China and around the world, outdoor cultivation has often suffered from severe yield reduction and even a failure of fruiting bodies to be produced for unknown reasons (Sambyal and Singh, 2021;Tan et al., 2021;Yu et al., 2022). Some studies have shown that possible reasons leading to the failure of morel fructification include unstable quality of spawn, improper field management practices, unfavorable environmental factors, pathogens, soil characteristics, soil microbial community dynamics, etc. (Zhao et al., 2016;He et al., 2017He et al., , 2018Lan et al., 2020;Wang et al., 2020;Tan et al., 2021;Yu et al., 2022). In fact, the obstacles associated with continuous cropping is also an important reason for the decline in morel yield. ...
Morels (Morchella spp.) are highly prized and popular edible mushrooms. The outdoor cultivation of morels in China first developed at the beginning of the 21st century. Several species, such as Morchella sextelata, M. eximia, and M. importuna, have been commercially cultivated in greenhouses. However, the detriments and obstacles associated with continuous cropping have become increasingly serious, reducing yields and even leading to a complete lack of fructification. It has been reported that the obstacles encountered with continuous morel cropping may be related to changes in the soil microbial community. To study the effect of dazomet treatment on the cultivation of morel under continuous cropping, soil was fumigated with dazomet before morel sowing. Alpha diversity and beta diversity analysis results showed that dazomet treatment altered the microbial communities in continuous cropping soil, which decreased the relative abundance of soil-borne fungal pathogens, including Paecilomyces, Trichoderma, Fusarium, Penicillium, and Acremonium, increased the relative abundance of beneficial soil bacteria, including Bacillius and Pseudomonas. In addition, the dazomet treatment significantly increased the relative abundance of morel mycelia in the soil and significantly improved morel yield under continuous cropping. These results verified the relationship between the obstacles associated with continuous cropping in morels and the soil microbial community and elucidated the mechanism by which the obstacle is alleviated when using dazomet treatment.
... With the expansion of cultivation range and density of morel production, disease have become the main factor limiting its yield. Pileus rot disease (He et al. 2018a), stipe rot disease (Guo et al. 2016), white mold disease Wang et al. 2020;Chen et al. 2021), and cobweb disease (Lan et al. 2020) are currently considered to be the four most serious diseases in morel industry (Fig. 19). These fungal diseases occur to varying degrees in most cultivated areas at any time, threatening the production of morels and causes economic losses. ...
Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of –OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools
in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided.
Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward
many new fungal and fungus-derived products.
... The whole genome of P. penicillatus has been analyzed by Wang et al. (2020). It was found that a large number of chitinase-dominated carbohydrate enzymes were encoded within, including those involved in the biosynthesis of diophenylenediamine, aldehyde reductase, and NADPH-hydrate isomerase, which are involved in regulating P. penicillatus infection of morels (Brouwer et al. 2014;Zerillo et al. 2013). ...
Since morels were first successfully cultivated commercially in Sichuan in 2012, morel cultivation has expanded to more than 20 provinces in China. The highest yield currently reaches 15,000 kg/ha. Morel cultivation is characterized by its environmental friendliness, short cycle length, and high profit. However, the yield obtained is unstable which makes morel cultivation a high-risk industry. Although 10 production cycles have passed, there is still a gap between morel cultivation practice and our basic knowledge of morel biology. This mini-review concentrates on the development needs of morel cultivation. We illustrate the key techniques used in the large-scale commercial cultivation of morels and their relevant studies, including nutritional requirements, mechanisms of nutrient bag, soil type, vegetative and reproductive growth conditions, and disease control. This review will be a useful practical reference for the commercial artificial cultivation of morels and promoting the vital technologies required.
Key points
•Unstable yield still exists after commercial cultivation of morels realized.
•There is a gap between cultivation practice and our knowledge of morel biology.
•Key techniques are illustrated for morel cultivation practice.
... Commercial indoor cultivation of morels in the United States was completely abandoned due to bacterial contamination and reduced output [8], although recently, reports on indoor cultivation are reemerging [9]. In China, home to the world's largest outdoor cultivation of Morchella (over 1200 ha in 2015-2016), there have also been reports of infections caused by fungi, including Fusarium incarnatum-equiseti species complex [10], Diploöspora longispora [11], Paecilomyces penicillatus causing white mold disease and infecting cultivated M. importuna [12,13], as well as Cladobotryum protrusum [14], among other pathogens [15]. There are no sufficient studies regarding morel diseases in indoor cultivation systems to date. ...
The cultivation of morel mushrooms (Morchella spp.) outdoors or in controlled indoor systems is a relatively new practice, and infections are beginning to be observed. Infection of indoor-cultivated Morchella rufobrunnea initials (primordia) occurred at our research facilities in Israel. The mushroom initials turned brown, were covered with a dense white mycelium of a foreign fungus and were disintegrated soon after. The isolation of a fungal contaminant from the infected mushroom revealed small colonies with a pinkish spore zone on potato dextrose agar medium. Molecular identification using partial large subunit 28S ribosomal DNA and rRNA internal transcribed spacer sequences identified the fungus as Purpureocillium lilacinum. Inoculation of Morchella colony on agar plat with the isolated fungus caused browning and inhibition of mycelial growth. Inoculation of a healthy primordium with P. lilacinum spores resulted in its browning and deterioration. This is the first report of an infection of indoor-cultivated mushroom and the first showing P. lilacinum as a pathogen of morels.
... More recently the squalestatin S1 producing BGC from Aspergillus sp. Z5 was reported in Paecilomyces penicillatus [72] and halophilic marine fungus Eurotium rubrum [73]. The cluster of both A. affinis strains shared three out of four genes of squalestatin S1 BGC: the core enzyme farnesyl-diphosphate farnesyltransferase (squalene synthase), a DnaJ domain protein and other one conserved hypothetical protein. ...
Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis's strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, L-pyroglutamic acid, lecanoric acid), antifungal (e.g., L-pyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati.
... Morels cultivated in ordinary farmland soils have been reported to suffer from various soil-borne pathogens (He et al., 2017(He et al., , 2018Lan et al., 2020;Wang et al., 2020). Besides, morel farmers also reported many cases of severe decreases in morel yield that were suspected as relating to abuse of fungicide, herbicide, and pesticide. ...
Black morel, a widely prized culinary delicacy, was once an uncultivable soil-saprotrophic ascomycete mushroom that can now be cultivated routinely in farmland soils. It acquires carbon nutrients from an aboveground nutritional supplementation, while it remains unknown how the morel mycelium together with associated microbiota in the substratum metabolizes and accumulates specific nutrients to support the fructification. In this study, a semi-synthetic substratum of quartz particles mixed with compost was used as a replacement and mimic of the soil. Two types of composts (C1 and C2) were used, respectively, plus a bare-quartz substratum (NC) as a blank reference. Microbiota succession, substrate transformation as well as the activity level of key enzymes were compared between the three types of substrata that produced quite divergent yields of morel fruiting bodies. The C1 substratum, with the highest yield, possessed higher abundances of Actinobacteria and Chloroflexi. In comparison with C2 and NC, the microbiota in C1 could limit over-expansion of microorganisms harboring N-fixing genes, such as Cyanobacteria, during the fructification period. Driven by the microbiota, the C1 substratum had advantages in accumulating lipids to supply morel fructification and maintaining appropriate forms of nitrogenous substances. Our findings contribute to an increasingly detailed portrait of microbial ecological mechanisms triggering morel fructification.
... White mold reduces production and quality of morels during cultivation, storage, and transportation [11]. White mold is highly adaptable, and has the ability of rapid colonization and transmission [11,17], which made it difficult to control without affecting morel production. The pathogenic mechanism of P. penicillatus and the related resistance mechanism of morels have not been fully understood [17]. ...
... White mold is highly adaptable, and has the ability of rapid colonization and transmission [11,17], which made it difficult to control without affecting morel production. The pathogenic mechanism of P. penicillatus and the related resistance mechanism of morels have not been fully understood [17]. ...
... The genomes of four Paecilomyces species (P. penicillatus CCMJ2836 [17], P. variotii CBS144490 HYG1 [20], P. variotii CBS 101075 [20], and P. niveus CO7 [21]) have been published. However, different fungal strains varied greatly in genome size, gene number and gene sequence. ...
Paecilomyces penicillatus is one of the pathogens of morels, which greatly affects the yield and quality of Morchella spp.. In the present study, we de novo assembled the genome sequence of the fungus P. penicillatus SAAS_ppe1. We analyzed the transcriptional profile of P. penicillatus SAAS_ppe1 infection of Morchella importuna at different stages (3 days and 6 days after infection) and the response of M. importuna using the transcriptome. The assembled genome sequence of P. penicillatus SAAS_ppe1 was 39.78 Mb in length (11 scaffolds; scaffold N50, 6.50 Mb), in which 99.7% of the expected genes were detected. A total of 7.48% and 19.83% clean transcriptional reads from the infected sites were mapped to the P. penicillatus genome at the early and late stages of infection, respectively. There were 3,943 genes differently expressed in P. penicillatus at different stages of infection, of which 24 genes had increased expression with the infection and infection stage, including diphthamide biosynthesis, aldehyde reductase, and NAD (P)H-hydrate epimerase (P < 0.05). Several genes had variable expression trends at different stages of infection, indicating P. penicillatus had diverse regulation patterns to infect M. importuna. GO function, involving cellular components, and KEGG pathways, involving glycerolipid metabolism, and plant-pathogen interaction were significantly enriched during infection by P. penicillatus. The expression of ten genes in M. importuna increased during the infection and infection stage, and these may regulate the response of M. importuna to P. penicillatus infection. This is the first comprehensive study on P. penicillatus infection mechanism and M. importuna response mechanism, which will lay a foundation for understanding the fungus-fungus interactions, gene functions, and variety breeding of pathogenic and edible fungi.
Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochon-drial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.
As one of the most nutritious and delicious mushroom varieties, Volvariella volvacea has always been popular among people around the world. Different from other artificially cultivated mushrooms, Volvariella volvacea is mostly planted on non-sterile substrates. As the cultivation time increases, the yield of mushroom houses continues to decrease. In our experiment, we selected two groups of samples from the old and new mushroom houses, environmental samples and substrate samples. The results showed that the diversity and abundance of microorganisms in the culture environment of the old mushroom room were consistent with that of the new mushroom room, but the proportion of actinomycetes in the former was significantly higher than that of the new mushroom room. The metabolic activity of microorganisms in the old mushroom room was enhanced compared with the new mushroom room. The microbial diversity in the growth substrate was investigated, and it was found that the structure and diversity of the microbial community in the substrate had changed. In conclusion, the interplay between mushrooms, the culture environment, and the host bacterial community may be the cause of the changes in the yield of Volvariella volvacea.
