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Granados-Casas AO, Sastoque AP, Stchigel AM, Fernández-Bravo A, Cano-Lira JF. Hybrid De Novo Whole-Genome Assembly, Annotation, and Identification of Secondary Metabolite Gene Clusters in the Ex-Type Strain of Chrysosporium keratinophilum. J Fungi (Basel) 2023; 9:jof9040389. [PMID: 37108844 PMCID: PMC10145314 DOI: 10.3390/jof9040389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Chrysosporium is a polyphyletic genus belonging (mostly) to different families of the order Onygenales (Eurotiomycetes, Ascomycota). Certain species, such as Chrysosporium keratinophilum, are pathogenic for animals, including humans, but are also a source of proteolytic enzymes (mainly keratinases) potentially useful in bioremediation. However, only a few studies have been published regarding bioactive compounds, of which the production is mostly unpredictable due to the absence of high-quality genomic sequences. During the development of our study, the genome of the ex-type strain of Chrysosporium keratinophilum, CBS 104.66, was sequenced and assembled using a hybrid method. The results showed a high-quality genome of 25.4 Mbp in size spread across 25 contigs, with an N50 of 2.0 Mb, 34,824 coding sequences, 8002 protein sequences, 166 tRNAs, and 24 rRNAs. The functional annotation of the predicted proteins was performed using InterProScan, and the KEGG pathway mapping using BlastKOALA. The results identified a total of 3529 protein families and 856 superfamilies, which were classified into six levels and 23 KEGG categories. Subsequently, using DIAMOND, we identified 83 pathogen-host interactions (PHI) and 421 carbohydrate-active enzymes (CAZymes). Finally, the analysis using AntiSMASH showed that this strain has a total of 27 biosynthesis gene clusters (BGCs), suggesting that it has a great potential to produce a wide variety of secondary metabolites. This genomic information provides new knowledge that allows for a deeper understanding of the biology of C. keratinophilum, and offers valuable new information for further investigations of the Chrysosporium species and the order Onygenales.
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Affiliation(s)
- Alan Omar Granados-Casas
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Angie Paola Sastoque
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Alberto Miguel Stchigel
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - Ana Fernández-Bravo
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
| | - José Francisco Cano-Lira
- Mycology Unit, Medical School, Universitat Rovira i Virgili, C/Sant Llorenç 21, 43201 Reus, Spain
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Host–Pathogen Interactions between Metarhizium spp. and Locusts. J Fungi (Basel) 2022; 8:jof8060602. [PMID: 35736085 PMCID: PMC9224550 DOI: 10.3390/jof8060602] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 01/27/2023] Open
Abstract
The progress in research on the interactions between Metarhizium spp. and locusts has improved our understanding of the interactions between fungal infection and host immunity. A general network of immune responses has been constructed, and the pathways regulating fungal pathogenicity have also been explored in depth. However, there have been no systematic surveys of interaction between Metarhizium spp. and locusts. The pathogenesis of Metarhizium comprises conidial attachment, germination, appressorial formation, and colonization in the body cavity of the host locusts. Meanwhile, the locust resists fungal infection through humoral and cellular immunity. Here, we summarize the crucial pathways that regulate the pathogenesis of Metarhizium and host immune defense. Conidial hydrophobicity is mainly affected by the contents of hydrophobins and chitin. Appressorial formation is regulated by the pathways of MAPKs, cAMP/PKA, and Ca2+/calmodulin. Lipid droplets degradation and secreted enzymes contributed to fungal penetration. The humoral response of locust is coordinated by the Toll pathway and the ecdysone. The regulatory mechanism of hemocyte differentiation and migration is elusive. In addition, behavioral fever and density-dependent population immunity have an impact on the resistance of hosts against fungal infection. This review depicts a prospect to help us understand host–pathogen interactions and provides a foundation for the engineering of entomopathogenic fungi and the discovery of insecticidal targets to control insect pests.
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Zhang L, Yue Q, Wang C, Xu Y, Molnár I. Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome. Nat Prod Rep 2021; 37:1164-1180. [PMID: 32211677 DOI: 10.1039/d0np00007h] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: 2014 up to the third quarter of 2019 Hypocrealean entomopathogenic fungi (HEF) produce a large variety of secondary metabolites (SMs) that are prominent virulence factors or mediate various interactions in the native niches of these organisms. Many of these SMs show insecticidal, immune system modulatory, antimicrobial, cytotoxic and other bioactivities of clinical or agricultural significance. Recent advances in whole genome sequencing technologies and bioinformatics have revealed many biosynthetic gene clusters (BGCs) potentially involved in SM production in HEF. Some of these BGCs are now well characterized, with the structures of the cognate product congeners elucidated, and the proposed biosynthetic functions of key enzymes validated. However, the vast majority of HEF BGCs are still not linked to SM products ("orphan" BGCs), including many clusters that are not expressed (silent) under routine laboratory conditions. Thus, investigations into the encoded parvome (the secondary metabolome predicted from the genome) of HEF allows the discovery of BGCs for known SMs; uncovers novel metabolites based on the BGCs; and catalogues the predicted SM biosynthetic potential of these fungi. Herein, we summarize new developments of the field, and survey the polyketide, nonribosomal peptide, terpenoid and hybrid SM BGCs encoded in the currently available 40 HEF genome sequences. Studying the encoded parvome of HEF will increase our understanding of the multifaceted roles that SMs play in biotic and abiotic interactions and will also reveal biologically active SMs that can be exploited for the discovery of human and veterinary drugs or crop protection agents.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Qun Yue
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.
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St. Leger RJ, Wang JB. Metarhizium: jack of all trades, master of many. Open Biol 2020; 10:200307. [PMID: 33292103 PMCID: PMC7776561 DOI: 10.1098/rsob.200307] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The genus Metarhizium and Pochonia chlamydosporia comprise a monophyletic clade of highly abundant globally distributed fungi that can transition between long-term beneficial associations with plants to transitory pathogenic associations with frequently encountered protozoans, nematodes or insects. Some very common 'specialist generalist' species are adapted to particular soil and plant ecologies, but can overpower a wide spectrum of insects with numerous enzymes and toxins that result from extensive gene duplications made possible by loss of meiosis and associated genome defence mechanisms. These species use parasexuality instead of sex to combine beneficial mutations from separate clonal individuals into one genome (Vicar of Bray dynamics). More weakly endophytic species which kill a narrow range of insects retain sexuality to facilitate host-pathogen coevolution (Red Queen dynamics). Metarhizium species can fit into numerous environments because they are very flexible at the genetic, physiological and ecological levels, providing tractable models to address how new mechanisms for econutritional heterogeneity, host switching and virulence are acquired and relate to diverse sexual life histories and speciation. Many new molecules and functions have been discovered that underpin Metarhizium associations, and have furthered our understanding of the crucial ecology of these fungi in multiple habitats.
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Xu R, Liu X, Peng B, Liu P, Li Z, Dai Y, Xiao S. Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism. Pathogens 2020; 9:pathogens9030232. [PMID: 32245129 PMCID: PMC7157644 DOI: 10.3390/pathogens9030232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
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.
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Affiliation(s)
- Rong Xu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xiaochen Liu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Peibin Liu
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zhuang Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China;
| | - Yueting Dai
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- Correspondence: (Y.D.); (S.X.); Tel.: +86-431-8453-2989 (Y.D. & S.X.)
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China; (R.X.); (B.P.)
- Correspondence: (Y.D.); (S.X.); Tel.: +86-431-8453-2989 (Y.D. & S.X.)
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Inglis GD, Duke GM, Goettel MS, Kabaluk JT, Ortega-Polo R. Biogeography and genotypic diversity of Metarhizium brunneum and Metarhizium robertsii in northwestern North American soils. Can J Microbiol 2019; 65:261-281. [DOI: 10.1139/cjm-2018-0297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The biogeography and genotype diversity of Metarhizium species in northwestern North American soils was examined; 20 ecoregions were sampled, including 58 agricultural and 80 natural habitat subsites, and areas that were glaciated during the Pleistocene epoch. One hundred and twenty-nine isolates of M. brunneum, 26 isolates of M. robertsii, four isolates of M. guizhouense, one isolate of M. flavoviride, and 55 isolates of Beauveria were recovered. Metarhizium and Beauveria species were isolated in diverse ecoregions within the study area, but a trend for increased isolation of Metarhizium species in western regions of the study area was observed. Consistent with this observation, the prevalence of M. brunneum and M. robertsii decreased at higher elevations, and the opposite was true for Beauveria. Both M. brunneum and M. robertsii were more commonly isolated from agricultural and natural habitat subsites, and considerable genotypic diversity was observed in both habitats and within the same subsite. Metarhizium robertsii, but not M. brunneum, was more commonly isolated from nonglaciated locations; however, less diversity and richness was observed for M. brunneum recovered from glaciated versus nonglaciated locations consistent with insular biogeography. The study has implications for microbial control strategies in the region.
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Affiliation(s)
| | - Grant M. Duke
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Mark S. Goettel
- Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - J. Todd Kabaluk
- Agriculture and Agri-Food Canada, Agassiz, BC V0M 1A0, Canada
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Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom. Genes (Basel) 2019; 10:genes10020124. [PMID: 30744046 PMCID: PMC6409746 DOI: 10.3390/genes10020124] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 02/06/2023] Open
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.
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Wang C, Wang S. Insect Pathogenic Fungi: Genomics, Molecular Interactions, and Genetic Improvements. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:73-90. [PMID: 27860524 DOI: 10.1146/annurev-ento-031616-035509] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Entomopathogenic fungi play a pivotal role in the regulation of insect populations in nature, and representative species have been developed as promising environmentally friendly mycoinsecticides. Recent advances in the genome biology of insect pathogenic fungi have revealed genomic features associated with fungal adaptation to insect hosts and different host ranges, as well as the evolutionary relationships between insect and noninsect pathogens. By using species in the Beauveria and Metarhizium genera as models, molecular biology studies have revealed the genes that function in fungus-insect interactions and thereby contribute to fungal virulence. Taken together with efforts toward genetic improvement of fungal virulence and stress resistance, knowledge of entomopathogenic fungi will potentiate cost-effective applications of mycoinsecticides for pest control in the field. Relative to our advanced insights into the mechanisms of fungal pathogenesis in plants and humans, future studies will be necessary to unravel the gene-for-gene relationships in fungus-insect interactive models.
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Affiliation(s)
- Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; ,
| | - Sibao Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; ,
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Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE. PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. Nucleic Acids Res 2017; 45:D604-D610. [PMID: 27915230 PMCID: PMC5210566 DOI: 10.1093/nar/gkw1089] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/24/2016] [Accepted: 10/27/2016] [Indexed: 11/14/2022] Open
Abstract
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed.
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Affiliation(s)
- Martin Urban
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Alayne Cuzick
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Kim Rutherford
- Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, Cambridgeshire CB2 1GA, UK
| | - Alistair Irvine
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Helder Pedro
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Rashmi Pant
- Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, India
| | - Vidyendra Sadanadan
- Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, India
| | - Lokanath Khamari
- Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, India
| | - Santoshkumar Billal
- Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, India
| | - Sagar Mohanty
- Molecular Connections Private Limited, Basavanagudi, Bangalore 560 004, India
| | - Kim E Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
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