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| Phylogenetic tree of members of the order Polyporales based on 179 highly conserved proteins. S. lacrymans (order Russulales) and H. annosum (order Boletales) were used as outgroup to root the tree. The strains of R. placenta cluster closely together, as expected for closely related strains (orange box).
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Brown rot fungi, such as Rhodonia placenta (previously Postia placenta), occur naturally in northern coniferous forest ecosystems and are known to be the most destructive group of decay fungi, degrading wood faster and more effectively than other wood-degrading organisms. It has been shown that brown rot fungi not only rely on enzymatic degradation...
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... species phylogeny was reconstructed using highly conserved gene products of the previously published genome annotations of the species indicated in Figure 5 ( Martinez et al., 2009;Eastwood et al., 2011;Fernandez-Fueyo et al., 2012;Floudas et al., 2012;Olson et al., 2012;Suzuki et al., 2012;Tang et al., 2012;Binder et al., 2013;Ohm et al., 2014;Nagy et al., 2015;Miettinen et al., 2016;Wu et al., 2018;Casado López et al., 2019). BUSCO v2 (dataset "fungi_odb9") was used to select 179 highly conserved proteins for the species phylogeny ( Simão et al., 2015). ...
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... phylogenetic tree based on 179 highly conserved gene products shows that both R. placenta strains are closely related. The evolutionary distance between them is similar to the distance between strains of Lentinus tigrinus and Dichomitus squalens ( Figure 5). ...
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... in important genes are one explanation for the differences seen in phenotype between the two species, but also regulatory mechanisms are likely having a powerful impact. The two genomes are closely related with a total identity of 98.4% and as confirmed by a phylogenetic analysis (Figure 5). The results of the variant analysis nevertheless showed a high number of The table includes the percentage of bases affected, relative to the total protein length and the number of AACs, as well as the protein. ...
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... species phylogeny was reconstructed using highly conserved gene products of the previously published genome annotations of the species indicated in Figure 5 ( Martinez et al., 2009;Eastwood et al., 2011;Fernandez-Fueyo et al., 2012;Floudas et al., 2012;Olson et al., 2012;Suzuki et al., 2012;Tang et al., 2012;Binder et al., 2013;Ohm et al., 2014;Nagy et al., 2015;Miettinen et al., 2016;Wu et al., 2018;Casado López et al., 2019). BUSCO v2 (dataset "fungi_odb9") was used to select 179 highly conserved proteins for the species phylogeny ( Simão et al., 2015). ...
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... phylogenetic tree based on 179 highly conserved gene products shows that both R. placenta strains are closely related. The evolutionary distance between them is similar to the distance between strains of Lentinus tigrinus and Dichomitus squalens ( Figure 5). ...
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... in important genes are one explanation for the differences seen in phenotype between the two species, but also regulatory mechanisms are likely having a powerful impact. The two genomes are closely related with a total identity of 98.4% and as confirmed by a phylogenetic analysis (Figure 5). The results of the variant analysis nevertheless showed a high number of The table includes the percentage of bases affected, relative to the total protein length and the number of AACs, as well as the protein. ...
Citations
... However, current data do not suggest any correlation between the presence of the SNVs found and the biocontrol capacity of PO212 nor the absence or presence of extra genes specifically related to this phenotype. Genome comparisons of Postia placenta strains evidenced high similarity between their genomes while showing important differences in phenotypes (Kölle et al., 2020). Hence, the high conservation of PO212 and S27 genomic sequences points to the presence of specific variants located in non-coding regions as candidates for a role in biocontrol. ...
Penicillium rubens strain 212 (PO212) is a filamentous fungus belonging to the division Ascomycete. PO212 acts as an effective biocontrol agent against several pathogens in a variety of horticultural crops including Fusarium oxysporum f.sp. lycopersici, causing vascular wilt disease in tomato plants. We assembled draft genomes of two P. rubens strains, the biocontrol agent PO212 and the soil isolate S27, which lacks biocontrol activity. We also performed comparative analyses of the genomic sequence of PO212 with that of the other P. rubens and P. chrysogenum strains. This is the first Penicillium strain with biocontrol activity whose genome has been sequenced and compared. PO212 genome size is 2,982 Mb, which is currently organized into 65 scaffolds and a total of 10,164 predicted Open Reading Frames (ORFs). Sequencing confirmed that PO212 belongs to P. rubens clade. The comparative analysis of the PO212 genome with the genomes of other P. rubens and Penicillium chrysogenum strains available in databases showed strong conservation among genomes, but a correlation was not found between these genomic data and the biocontrol phenotype displayed by PO212. Finally, the comparative analysis between PO212 and S27 genomes showed high sequence conservation and a low number of variations mainly located in ORF regions. These differences found in coding regions between PO212 and S27 genomes can explain neither the biocontrol activity of PO212 nor the absence of such activity in S27, opening a possible avenue toward transcriptomic and epigenetic studies that may shed light on this mechanism for fighting plant diseases caused by fungal pathogens. The genome sequences described in this study provide a useful novel resource for future research into the biology, ecology, and evolution of biological control agents.
... However, our results also suggest that amorphogenesis of cellulose is not caused by all brown-rot fungi. This could be related to differences between the degradation mechanisms across brown-rot fungi (47) or the environmental cues that regulate such mechanisms, but also additional factors such as the amount of time since the strain has been isolated in culture and whether the strain is dikaryotic or monokaryotic (48)(49)(50)(51). Moreover, cellulose amorphogenesis caused by Gloeophyllum sp. and L. leucothites does not seem to be merely the result of the Fenton reaction for two reasons. ...
Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose.
... MRSA isolates were characterized by nucA and coagulase profiles and identified using Vitek 2 identification cards. Details of their growth conditions and isolation have been described previously (4,5). The isolates were grown in tryptic soy broth (TSB) (Thermo Fisher Scientific, Waltham, MA) at 35°C for 18 h, and the pellet was obtained after centrifugation at 10,000 Â g for 5 min. ...
Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogenic bacterium responsible for difficult-to-treat staphylococcal infections due to multidrug resistance. Twelve Panton-Valentine leucocidin (PVL)-positive and multidrug-resistant clinical MRSA isolates from hospitals in Pakistan were sequenced and annotated to investigate genetic markers associated with antimicrobial resistance, virulence, and biofilm formation.
... & Schigel (also known as Postia placenta) FPRL280 and MAD-698, as well as G. trabeum (Pers.) Murrill, all of them presenting different phenotypes (Thaler et al., 2012;Presley and Schilling, 2017;Kölle et al., 2020). The brown rot fungi R. placenta and G. trabeum are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures (Niemenmaa et al., 2008). ...
... Furthermore, these findings will also be valuable for the development of new commercial applications for the degradation of lignocellulosic materials. Based on the previous genome comparison of the two R. placenta strains (Kölle et al., 2020), differences in overall gene expression should further elaborate the adapted degradation mechanisms between them. ...
... Gene expression was analyzed using CLC Genomic Workbench v. 20.0.4 (Qiagen). Reads were mapped against the corresponding genomes (Floudas et al., 2012;Kölle et al., 2020), while the MAD-698 transcriptome data were mapped to the monokaryotic genome of MAD-SB12 (Gaskell et al., 2017). Mapping statistics can be found in Supplementary Material 3. MAD-SB12 genome was used as reference following previous results by Kölle et al. (2020). ...
Brown rot fungi degrade wood in a two-step process in which enzymatic hydrolysis is preceded by an oxidative degradation phase. While a detailed understanding of the molecular processes during brown rot decay is mandatory for being able to better protect wooden products from this type of degradation, the underlying mechanisms are still not fully understood. This is particularly true for wood that has been treated to increase its resistance against rot. In the present study, the two degradation phases were separated to study the impact of wood acetylation on the behavior of three brown rot fungi commonly used in wood durability testing. Transcriptomic data from two strains of Rhodonia placenta (FPRL280 and MAD-698) and Gloeophyllum trabeum were recorded to elucidate differences between the respective decay strategies. Clear differences were found between the two decay stages in all fungi. Moreover, strategies varied not only between species but also between the two strains of the same species. The responses to wood acetylation showed that decay is generally delayed and that parts of the process are attenuated. By hierarchical clustering, we could localize several transcription factors within gene clusters that were heavily affected by acetylation, especially in G. trabeum. The results suggest that regulatory circuits evolve rapidly and are probably the major cause behind the different decay strategies as observed even between the two strains of R. placenta. Identifying key genes in these processes can help in decay detection and identification of the fungi by biomarker selection, and also be informative for other fields, such as fiber modification by biocatalysts and the generation of biochemical platform chemicals for biorefinery applications.
... It has been suggested that switching degradation behavior in hardwoods by decay fungi may be an adaption to degrading cells rich in the ratio of guaiacyl/syringyl lignin ( [12]; e.g., Fistulina hepatica; [51]; e.g., Coniophora puteana). However, it was reported [54] that difference between characterizations of monokaryotic (genotype) and dikaryotic (phenotype) strains could be one of the degradation behaviors for the fungi. ...
Fungal wood decay strategies are influenced by several factors, such as wood species, moisture content, and temperature. This study aims to evaluate wood degradation characteristics of spruce, beech, and oak after exposure to the white-rot fungi Pleurotus ostreatus and Trametes versicolor. Both fungi caused high mass losses in beech wood, while spruce and oak wood were more resistant to decay. The moisture content values of the decayed wood correlated with the mass losses for all three wood species and incubation periods. Combined microscopic and chemical studies indicated that the two fungi differed in their decay behavior. While T. versicolor produced a decay pattern (cell wall erosion) typical of white-rot fungi in all wood species, P. ostreatus caused cell wall erosion in spruce and beech and soft-rot type I (cavity formation) decay in oak wood. These observations suggest that P. ostreatus may have the capacity to produce a wider range of enzymes/radicals triggered by the chemical composition of wood cell walls and/or local compositional variability within the cell wall.
... It has been suggested that switching degradation behavior in hardwoods by decay fungi may be an adaption to degrading cells rich in the ratio of guaiacyl/syringyl lignin ( [12]; e.g., Fistulina hepatica; [51]; e.g., Coniophora puteana). However, it was reported [54] that difference between characterizations of monokaryotic (genotype) and dikaryotic (phenotype) strains could be one of the degradation behaviors for the fungi. ...
Metabolomics has been extensively used in clinical studies in the search for new biomarkers of human diseases. However, this approach has also been highlighted in agriculture and biological sciences, once metabolomics studies have been assisting researchers to deduce new chemical mechanisms involved in biological interactions that occur between microorganisms and plants. In this sense, the knowledge of the biological role of each metabolite (virulence factors, signaling compounds, antimicrobial metabolites, among others) and the affected biochemical pathways during the interaction contribute to a better understand of different ecological relationships established in nature. The current chapter addresses five different applications of the metabolomics approach in fungal-plant interactions research: (1) Discovery of biomarkers in pathogen-host interactions, (2) plant diseases diagnosis, (3) chemotaxonomy, (4) plant defense, and (5) plant resistance; using mass spectrometry and/or nuclear magnetic resonance spectroscopy, which are the techniques most used in metabolomics.
Dispersion and atmospheric transport of fungal bioaerosols help fungal migration and colonization worldwide. The particle size of fungal propagules mainly controls this and influences the taxonomic composition of fungal bioaerosols in a region. The study reports the size-resolved genomic characterization of the pathogenic and non-pathogenic fungal bioaerosols found in the Indian subcontinent. Scanning Electron Microscope images and results from size-resolved DNA analysis using the next-generation sequencing (NGS) method inferred the presence of unicellular and multi-cellular spores and large fungal fragments in the bioaerosols. Further investigations inferred the presence of 67 crop pathogenic fungal OTUs capable of causing lethal crop diseases threatening the country’s food security and agricultural economy. Many other pathogenic fungal species, which could affect plants (plants excluding the crops), humans, and insects were also found in the bioaerosols. About 176 non-pathogenic OTUs inferred the presence of some beneficial fungal species in bioaerosols. Community diversity and similarities shared by each pathogenic and non-pathogenic category implied that the pathogenic fungal categories shared many OTUs within the categories, compared to the non-pathogenic fungal categories, explicitly explaining the evolution potential of pathogenic fungal species to infect a broad host range. Such studies on bioaerosol characterization based on host-pathogen interactions help to predict pathogenic fungal invasions and help the government to ensure biosecurity.
Infections caused by hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) strains have higher morbidity and mortality rates and require longer hospital stays than do those caused by hospital-associated methicillin-sensitive Staphylococcus aureus strains. To gain insight into their genomic makeup, antimicrobial resistance, biofilm formation, and virulence potentials, here we present the draft whole-genome sequences of 27 HA-MRSA strains isolated in Minnesota.
