Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in <i>Clonostachys</i> subgenus <i>Bionectria</i> (Fungi, Ascomycota, Hypocreales)

Broberg, Martin; Dubey, Mukesh; Iqbal, Mudassir; Gudmundssson, Mikael; Ihrmark, Katarina; Schroers, Hans-Josef; Jensen, Dan Funck; Durling, Mikael Brandström; Karlsson, Magnus

doi:10.1111/eva.13134

Cited by 26 publications

(41 citation statements)

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“…Therefore, differences in expression and diversification of this gene family are potential contributors to the differentiation between detrimental and non-detrimental fungi in the A. thaliana root mycobiome, especially since A. thaliana cell-wall composition is a determinant factor for disease resistance 70 , 71 . Notably, expansion of the PL1_7 gene family was observed in plant pathogens but also in the biocontrol fungus C. rosea (Sordariomycetes, Hypocreales), a fungal species with mycoparasitic and plant endophytic capacity 72 , 73 that is phylogenetically closely related to multiple isolates selected in this study. Genetic manipulation of the C. rosea pel12 gene revealed a direct involvement of the protein in pectin degradation, but not in C. rosea biocontrol towards the phytopathogen Botrytis cinerea 57 .…”

Section: Discussionmentioning

confidence: 85%

Genetic determinants of endophytism in the Arabidopsis root mycobiome

et al. 2021

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The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

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Section: Discussionmentioning

confidence: 85%

Genetic determinants of endophytism in the Arabidopsis root mycobiome

et al. 2021

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“…The other detected differentially expressed MFS transporters are commonly involved in efflux-mediated protection against exogenous or endogenous secondary metabolites and sugar uptake, suggesting a DCL-dependent influence on this aspect of C. rosea mycoparasitic action. This group also includes nine genes belonging to the drug–H + antiporter-2 family, which underwent a significant gene expansion during C. rosea evolution and has therefore a putative important role in the fungus lifestyle ( 79 ). DCL-based control of these transporters is most likely indirect because most MFS genes detected in this way are downregulated in the mutants, whereas direct targets of RNA silencing are expected to be upregulated after dcl deletion.…”

Section: Discussionmentioning

confidence: 99%

Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions

et al. 2021

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“…To evaluate milRNA conservation in the genus Clonostachys , subgenus Bionectria , we searched for milRNA precursor sequences in genomes of five other species sequenced until date (48). Among the 74 milRNAs observed in this study and in that of (41), nine milRNAs were detected in at least five of the six Clonostachys spp, while 44 were detected in at least one more Clonostachys sp.…”

Section: Resultsmentioning

confidence: 99%

Comparative small RNA and degradome sequencing provide new insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea

Piombo

Vetukuri

Sundararajan

et al. 2022

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Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small-RNAs (sRNAs) are vital components of post-transcriptional gene regulation, although their role in gene expression regulation during mycoparasitism remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tags sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were down-regulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing de-suppression (up-regulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated gene targets for 282 differentially expressed sRNAs. Analysis of sRNA gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. While the regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum highlighting common and mycohosts-specific gene regulation of C. rosea. By combining these results with transcriptome data collected in similar experimental conditions during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism.

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Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 26 publications

References 156 publications

Genetic determinants of endophytism in the Arabidopsis root mycobiome

Genetic determinants of endophytism in the Arabidopsis root mycobiome

Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions

Comparative small RNA and degradome sequencing provide new insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea

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