DFVF: database of fungal virulence factors

Tao, Lu; Bo, Yao; Zhang, Chi

doi:10.1093/database/bas032

Cited by 86 publications

(51 citation statements)

References 20 publications

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“…Protease candidates were screened by searching secretory proteins against the MEROPS database [69]. Pathogenic genes were identified using the PHI (http://www.phi-base.org/) [70] and DFVF (http://sysbio.unl.edu/ DFVF/Download.php) [71] databases. Effector candidates were predicted in combination with the SignalP 5.0 server (http://www.cbs.dtu.dk/services/SignalP-5.0/).…”

Section: Secretome Analysis and Pathogenicity-related Genesmentioning

confidence: 99%

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

Liu

Peng

et al. 2020

Pathogens

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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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Section: Secretome Analysis and Pathogenicity-related Genesmentioning

confidence: 99%

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

Liu

Peng

et al. 2020

Pathogens

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“…The analysis of the protein family expansion and contraction was performed with the CAFE 3.0 software (Han et al 2013). Three tables of protein families/clusters were used as input: (i) the numbers of proteins with a specific Pfam domain in each proteome, for each Pfam motif found by the stand-alone Pfam scanner and a database downloaded on 8 July, 2015 (Punta et al 2012); (ii) the numbers of blast hits in each proteome (e-value cut-off, 1 9 e -20 ) where proteins from the Database of Fungal Virulence Factors [downloaded on 7 July, 2015; (Lu et al 2012)] were used as queries; (iii) the numbers of blast hits in each proteome (e-value cut-off, 1 9 e -20 ) where proteins from the core set of the Fungal Stress Response Database [received from the authors on 4 March, 2015; (Karanyi et al 2013)] were used as queries. The resulting list of protein groups with significant predicted expansion/contraction was manually checked with a focus on the branches leading to A. melanogenum, H. werneckii and E. dermatitidis.…”

Section: Cafe Analysismentioning

confidence: 99%

Fungi between extremotolerance and opportunistic pathogenicity on humans

et al. 2018

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Numerous agents of infections in humans and other mammals are found among fungi that are able to survive extreme environmental conditions and to quickly adapt to novel habitats. Nevertheless, the relationship between opportunistic potential and polyextremotolerance was not yet studied systematically in fungi. Here, the link between polyextremotolerance and opportunistic pathogenicity is shown in a kingdom-wide phylogenetic analysis as a statistically significant cooccurrence of extremotolerance (e.g. osmotolerance and psychrotolerance) and opportunism at the level of fungal orders. In addition to extremotolerance, fungal opportunists share another characteristic-an apparent lack of specialised virulence traits. This is illustrated by a comparative genomic analysis of 20 dothideomycetous and eurotiomycetous black fungi. While the genomes of specialised fungal plant pathogens were significantly enriched in known virulence-associated genes that encode secreted proteases, carbohydrate active enzyme families, polyketide synthases, and non-ribosomal peptide synthetases, no such signatures were observed in human opportunists. Together the presented results have several implications. If infection of human hosts is a side effect of fungal stress tolerance and adaptability, the human body is most likely neither the preferred habitat of such species, nor important for their evolutionary success. This defines opportunism as opposed to pathogenicity, where infection is advantageous for the species' fitness. Since opportunists are generally incapable of the host-to-host transmission, any host-specific adaptations are likely to be lost with the resolution of the infection, explaining the observed lack of specialised virulence traits. In this scenario opportunistic infections should be seen as an evolutionary dead end and unlikely to lead to true pathogenicity.

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“…It includes over 570 primer sets for more than 200 species of phytopathogenic fungi. DFVF [182] is a database of fungal virulence factors, and includes information on 2,058 genes of fungal pathogens.…”

Section: Databasesmentioning

confidence: 99%

Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Cuadros-Orellana¹

2013

Fungal Genom Biol

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Fungi are ubiquitous inhabitants of soil and aquatic environments, and they establish and maintain either parasitic or symbiotic relationships with animals and plants. They are major players in nutrient cycling, especially in organic matter decomposition, and they are major sources of biologically active substances. However, their full metabolic potential is yet to be unveiled, and fungal enzymes could be of great use in myriad of applications from industrial processes to natural products. The global number of species in the fungal kingdom has been estimated in the range of one to a few million, but it is likely larger, as suggested by recent metagenomic studies that revealed the existence of fungal diversity hotspots. In this review, we describe the main advances in the study of fungal diversity, present statistics of the main metagenomic databases with regard to the representativeness of fungal phyla, and discuss the future directions in this field.

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DFVF: database of fungal virulence factors

Cited by 86 publications

References 20 publications

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

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

Fungi between extremotolerance and opportunistic pathogenicity on humans

Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

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