Improving the Genome Annotation of Rhizoctonia solani Using Proteogenomics

2021 ◽  
Vol 22 ◽  
Author(s):  
Jiantao Shu ◽  
Mingkun Yang ◽  
Cheng Zhang ◽  
Pingfang Yang ◽  
Feng Ge ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Genome Annotation ◽  
Crop Production ◽  
Pathogenic Fungus ◽  
Single Amino Acid ◽  
Genomic Information ◽  
Post Translational Modifications ◽  
Homologous Sequences ◽  
Host Interaction ◽  
Pathogenic Genes

Background: Rhizoctonia solani is a pathogenic fungus that causes serious diseases in many crops, including rice, wheat, and soybeans. In crop production, it is very important to understand the pathogenicity of this fungus, which is still elusive. It might be helpful to comprehensively understand its genomic information using different genome annotation strategies. Methods: Aiming to improve the genome annotation of R. solani, we performed a proteogenomic study based on the existing data. Based on our study, a total of 1060 newly identified genes, 36 revised genes, 139 single amino acid variants (SAAVs), 8 alternative splicing genes, and diverse post-translational modifications (PTMs) events were identified in R. solani AG3. Further functional annotation on these 1060 newly identified genes was performed through homology analysis with its 5 closest relative fungi. Results: Based on this, 2 novel candidate pathogenic genes, which might be associated with pathogen-host interaction, were discovered. In addition, in order to increase the reliability and novelty of the newly identified genes in R. solani AG3, 1060 newly identified genes were compared with the newly published available R. solani genome sequences of AG1, AG2, AG4, AG5, AG6, and AG8. There are 490 homologous sequences. We combined the proteogenomic results with the genome alignment results and finally identified 570 novel genes in R. solani. Conclusion: These findings extended R. solani genome annotation and provided a wealth of resources for research on R. solani.

scholarly journals In situ Impact of the Antagonistic Fungal Strain, Trichoderma gamsii T30 on the Plant Pathogenic Fungus, Rhizoctonia solani in Soil

2019 ◽  
Vol 68 (2) ◽  
pp. 211-216
Author(s):  
MUHAMMAD ANEES ◽  
MUHAMMAD ABID ◽  
SOBIA CHOHAN ◽  
MUHAMMAD JAMIL ◽  
NADEEM AHMED ◽  
...  
Keyword(s):  
Population Density ◽  
Rhizoctonia Solani ◽  
Pathogenic Fungus ◽  
Suppressive Effect ◽  
Fungal Strain ◽  
Soil Microbiome ◽  
Target Dna ◽  
Wide Range ◽  
First Time

Rhizoctonia solani is a soil-borne fungus causing a wide range of plants diseases. Trichoderma gamsii strain T30 has previously been reported as antagonistic against R. solani. Although there are a few studies about the influence of Trichoderma strains on the R. solani densityin a pathosystem in the presence of plant hosts, this report for the first time comprehensively describes in situ effects of a T. gamsii strain on the population density of R. solani in the soil microcosmic conditions. The population dynamics of R. solani were followed in the autoclaved and non-autoclaved soils in artificially prepared microcosms up to day 25 after co-inoculation with T. gamsii in the variable ratios (R1/T1; R1/T0.1; R1/T0.01 of R. solani/T. gamsii). The population density of R. solani was evaluated by qPCR. In the autoclaved soil, target DNA copies of R. solani increased in the control samples from 1 × 105 to 6.5 × 106. At R1/T0.01, the number of target DNA copies were not significantly changed until day 11; however, it decreased by around five times at day 25. At R1/T0.1 and R1/T1, the number of DNA copies was reduced to 2.1 × 106 and 7.6 × 105 at day 11, respectively and the reduction was as much as 17 times at day 25. In the non-autoclaved soil, the number of the fungal cells decreased at day 25 whether inoculated or not with Trichoderma indicating a general suppression by the soil microbiome. In brief, T. gamsii significantly inhibited the growth of R. solani in the soil in situ and there was a general suppressive effect of the natural microbiome.

scholarly journals Temporal Interactions between Root-Lesion Nematodes and the Fungus Rhizoctonia Solani Lead to Reduced Potato Yield

Agronomy ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 361 ◽  
Author(s):  
Eva Edin ◽  
Mehreen Gulsher ◽  
Mikael Andersson Franko ◽  
Jan-Eric Englund ◽  
Adam Flöhr ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Tuber Yield ◽  
Pathogenic Fungus ◽  
Stem Canker ◽  
Fungal Mycelium ◽  
Lesion Nematodes ◽  
Fungal Damage ◽  
Root Lesion Nematodes ◽  
Temporal Interactions ◽  
Potato Crops

Soil microorganisms and soil fauna may have a large impact on the tuber yield of potato crops. The interaction between root-lesion nematodes and the pathogenic fungus Rhizoctonia solani Kühn was studied on potato plants grown in pots under controlled conditions. In two similar experiments, different combinations of nematodes and fungal mycelium were added to the pots at three occasions; at planting, after 14 days, and after 28 days. The nematodes reduced root biomass and the combination of nematodes and R. solani resulted in reduced tuber yield in both experiments, but the interaction was not synergistic. In contrast, the number of stem canker lesions decreased in the presence of nematodes compared to treatments with R. solani only. The time of inoculation influenced the severity of both fungal and nematode damage. The nematode damage on tubers was less severe if the nematodes were added at 28 days, while the number of severe stem canker lesions increased if the fungus was added at 28 days. However, the time of nematode inoculation did not affect the incidence of fungal damage, hence the nematodes did not assist R. solani to infect the plant. Our results highlight the underestimated importance of root-lesion nematodes, not resulting in obvious above ground symptoms or misshaped tubers yet affecting the performance of other pathogens.

scholarly journals Fungicide SYP-14288 Inducing Multidrug Resistance in Rhizoctonia solani

Plant Disease ◽  
2020 ◽  
Vol 104 (10) ◽  
pp. 2563-2570 ◽  
Author(s):  
Xingkai Cheng ◽  
Xuejing Man ◽  
Zitong Wang ◽  
Li Liang ◽  
Fan Zhang ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Rhizoctonia Solani ◽  
Parental Strain ◽  
Crop Production ◽  
Plant Pathogens ◽  
Economic Losses ◽  
Cross Resistance ◽  
Baseline Sensitivity ◽  
Rice Plants ◽  
Type Strains

Rhizoctonia solani is a widely distributed soilborne plant pathogen, and can cause significant economic losses to crop production. In chemical controls, SYP-14288 is highly effective against plant pathogens, including R. solani. To examine the sensitivity to SYP-14288, 112 R. solani isolates were collected from infected rice plants. An established baseline sensitivity showed that values of effective concentration for 50% growth inhibition (EC50) ranged from 0.0003 to 0.0138 μg/ml, with an average of 0.0055 ± 0.0030 μg/ml. The frequency distribution of the EC50 was unimodal and the range of variation factor (the ratio of maximal over minimal EC50) was 46.03, indicating that all wild-type strains were sensitive to SYP-14288. To examine the risk of fungicide resistance, 20 SYP-14288-resistant mutants were generated on agar plates amended with SYP-14288. Eighteen mutants remained resistant after 10 transfers, and their fitness was significantly different from the parental strain. All of the mutants grew more slowly but showed high virulence to rice plants, though lower than the parental strain. A cross-resistance assay demonstrated that there was a positive correlation between SYP-14288 and fungicides having or not having the same mode of action with SYP-14288, including fluazinam, fentin chloride, fludioxonil, difenoconazole, cyazofamid, chlorothalonil, and 2,4-dinitrophen. This result showed a multidrug resistance induced by SYP-14288, which could be a concern in increasing the spectrum of resistance in R. solani to commonly used fungicides.

Effect of non-antifungal agrochemicals on the pathogenic fungus Cryptococcus gattii

2019 ◽  
Vol 58 (1) ◽  
pp. 47-53 ◽  
Author(s):  
Hellem Cristina Silva Carneiro ◽  
Noelly Queiroz Ribeiro ◽  
Rafael Wesley Bastos ◽  
Daniel Assis Santos
Keyword(s):  
Crop Production ◽  
Pathogenic Fungus ◽  
Cryptococcus Gattii ◽  
Agricultural Products ◽  
Cross Resistance ◽  
Human Pathogens ◽  
High Concentrations ◽  
Susceptibility Tests ◽  
Susceptible Subpopulations

Abstract The chemical control of pests and weeds is employed to improve crop production and the quality of agricultural products. The intensive use of pesticides, however, may cause environmental contamination, thus altering microbial communities. Cryptococcus gattii is an environmental yeast and the causative agent of cryptococcosis in both humans and animals. Up to this day, the effects of agrochemicals on human pathogens living in nature are still widely unknown. In this work, we analyzed the susceptibility of C. gattii to nonfungicide agrochemicals (herbicides and insecticides). Microdilution and drug-combination susceptibility tests were performed for the herbicides flumioxazin (FLX), glyphosate (GLY), isoxaflutole (ISO), pendimethalin (PEND), and also for the insecticide fipronil (FIP). Moreover, these compounds were combined with the clinical antifungals amphotericin B and fluconazole. The MIC values found for the agrochemicals were the following: < 16 μg/ml, for flumioxazin; 128 to 256 μg/ml, for FIP, ISO, and PEND; and >256 μg/ml, for GLY. Synergistic and antagonistic interactions, depending on the strain and concentration tested, were also observed. All strains had undergone adaptation to increasing levels of agrochemicals, in order to select the less susceptible subpopulations. During this process, one C. gattii strain (196 L/03) tolerated high concentrations (50 to 900 μg/ml) of all pesticides assessed. Subsequently, the strain adapted to flumioxazin, isoxaflutole and pendimethalin showed a reduction in the susceptibility to agrochemicals and clinical antifungals, suggesting the occurrence of cross-resistance. Our data point to the risk of exposing C. gattii to agrochemicals existing in the environment, once it might impact the susceptibility of clinical antifungals.

scholarly journals Compositional diversity and evolutionary pattern of coronavirus accessory proteins

2020 ◽  
Author(s):  
Jingzhe Shang ◽  
Na Han ◽  
Ziyi Chen ◽  
Yousong Peng ◽  
Liang Li ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Regulatory Sequence ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Reading Frame ◽  
Evolutionary Pattern ◽  
Host Interaction ◽  
Sequence Recognition ◽  
Compositional Diversity

Abstract Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.

scholarly journals Microbial L-phenylalanine ammonia-lyase. Purification, subunit structure and kinetic properties of the enzyme from Rhizoctonia solani

1975 ◽  
Vol 149 (1) ◽  
pp. 65-75 ◽  
Author(s):  
K K Kalghatgi ◽  
P V Subba Rao
Keyword(s):  
Molecular Weight ◽  
Rhizoctonia Solani ◽  
Phenylalanine Ammonia Lyase ◽  
Pathogenic Fungus ◽  
Gradient Centrifugation ◽  
Hill Coefficient ◽  
Velocity Versus ◽  
Kinetic Properties ◽  
Subunit Structure ◽  
Protamine Sulphate

1. Phenylalanine ammonia-lyase (EC 4.3.1.5) was purified to homogeneity from the acetone-dried powders of the mycelial felts of the plant pathogenic fungus Rhizoctonia solani. 2. A useful modification in protamine sulphate treatment to get substantial purification of the enzyme in a single-step is described. 3. The purified enzyme shows bisubstrate activity towards L-phenylalanine and L-tyrosine. 4. It is sensitive to carbonyl reagents and the inhibition is not reversed by gel filtration. 5. The molecular weight of the enzyme as determined by Sephadex G-200 chromatography and sucrose-density-gradient centrifugation is around 330000. 6. The enzyme is made up of two pairs of unidentical subunits, with a molecular weight of 70000 (α) and 90000 (β) respectively. 7. Studies on initial velocity versus substrate concentration have shown significant deviations from Michaelis-Menten kinetics. 8. The double-reciprocal plots are biphasic (concave downwards) and Hofstee plots show a curvilinear pattern. 9. The apparent Km value increases from 0.18 mM to as high as 5.0 mM with the increase in the concentration of the substrate and during this process the Vmax, increases by 2-2.5-fold. 10. The value of Hill coefficient is 0.5. 11. Steady-state rates of phenylalanine ammonia-lyase reaction in the presence of inhibitors like D-phenylalanine, cinnamic, p-coumaric, caffeic, dihydrocaffeic and phenylpyruvic acid have shown that only one molecule of each type of inhibitor binds to a molecule of the enzyme. These observations suggest the involvement of negative homotropic interactions in phenylalanine ammonia-lyase. 12. The enzyme could not be desensitized by treatment with HgCl2, p-chloromercuribenzoic acid or by repeated freezing and thawing.

scholarly journals Proteogenomic characterization of the pathogenic fungus Aspergillus flavus reveals novel genes involved in aflatoxin production

2020 ◽  
pp. mcp.RA120.002144
Author(s):  
Mingkun Yang ◽  
Zhuo Zhu ◽  
Zhenhong Zhuang ◽  
Youhuang Bai ◽  
Shihua Wang ◽  
...  
Keyword(s):  
Aspergillus Flavus ◽  
Stress Responses ◽  
Splice Variants ◽  
Pathogenic Fungus ◽  
Aflatoxin Production ◽  
Mass Spectrometry Data ◽  
Single Amino Acid ◽  
High Quality ◽  
Novel Proteins ◽  
Wide Range

Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality dataset confirmed the translation of 8,724 previously-predicted genes, and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of post-translational modifications (PTMs), including 3,461 modification sites from 1,765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.

scholarly journals Characterization of Hydroxyproline-Containing Hairpin-Like Antimicrobial Peptide EcAMP1-Hyp from Barnyard Grass (Echinochloa crusgalli L.) Seeds: Structural Identification and Comparative Analysis of Antifungal Activity

2018 ◽  
Vol 19 (11) ◽  
pp. 3449 ◽  
Author(s):  
Eugene Rogozhin ◽  
Artur Zalevsky ◽  
Alexander Mikov ◽  
Alexey Smirnov ◽  
Tsezi Egorov
Keyword(s):  
Antifungal Activity ◽  
Plant Immunity ◽  
Pathogenic Fungus ◽  
Hyphal Growth ◽  
Single Amino Acid ◽  
Hydrophobic Core ◽  
Barnyard Grass ◽  
Vitro Binding ◽  
Dynamics Simulations

Herein, we describe a modified form of the antimicrobial hairpin-like peptide EcAMP1, isolated from barnyard grass (E. crusgalli) seeds, which is structurally characterized by a combination of high-pressure liquid chromatography, mass spectrometry, and automated Edman sequencing. This derivate has a single amino acid substitution (Pro19Hyp) in the second α-helical region of the molecule, which is critical for the formation of the hydrophobic core and the secondary structure elements. Comparing the antifungal activity of these two peptides, we found that the modified EcAMP1-Hyp had a significantly weaker activity towards the most-sensitive plant pathogenic fungus Fusarium solani. Molecular dynamics simulations and in vitro binding to the commercial polysaccharides allowed us to conclude that the Pro-19 residue is important for binding to carbohydrates located in the spore cell wall and it chiefly exhibits a fungistatic action representing the hyphal growth inhibition. These data are novel and significant for understanding a role of α-hairpinins in plant immunity.

scholarly journals Use of antigenic composition to differentiate among Rhizoctonia solani isolates from flax

2018 ◽  
Vol 44 (3) ◽  
pp. 415-421
Author(s):  
EM Hussein ◽  
AA Aly ◽  
Ola Ghel-Hawary ◽  
Heba I Mohamed ◽  
AA Mosa ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Host Range ◽  
Pathogenic Fungus ◽  
Double Diffusion ◽  
Antigenic Composition ◽  
Plant Pathogenic Fungus ◽  
Worldwide Distribution ◽  
Wide Host Range ◽  
Diffusion Technique ◽  
Highly Sensitive

Rhizoctonia solani is an plant pathogenic fungus with a wide host range and worldwide distribution. Double diffusion technique was used to differentiate among Rhizoctonia solani isolates from flax. In this technique, antisera of isolate 23 (AG-2) and isolate 24 (AG-4) reacted against antigens of 24 isolates belonging to AG-2 and Ag-4. The antiserum of isolate 23 (AG-2) was insensitive to differentiate among the isolates of AG-2, while it was highly sensitive to differentiate among some isolates of AG-4. The antiserum of isolate 24 (AG-4) was highly sensitive as a serotaxonomic tool to differentiate among AG-2 and AG-4, while it was of limited value in differentiating among isolates of within each AG.

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