Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea

Piombo, Edoardo; Vetukuri, Ramesh R.; Sundararajan, Poorva; Kushwaha, Sandeep; Jensen, Dan Funck; Karlsson, Magnus; Dubey, Mukesh

doi:10.1128/aem.00643-22

Cited by 7 publications

(3 citation statements)

References 91 publications

(143 reference statements)

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“…Among the fungal strains isolated, some studies exhibited intriguing attributes and mechanisms that could be involved in their disease-suppressive effects. For instance, C. rosea antagonizes Rhizoctonia solani [51], Verticillium wilt [52], and Meloidogyne spp. [53].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Soil Suppressiveness of Various Japanese Soils against the Soybean Cyst Nematode Heterodera glycines and Its Relation with the Soil Chemical and Biological Properties

Yang,

Wu,

Perry

et al. 2023

Agronomy

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This study aimed to evaluate the suppressive potential of different soils on soybean cyst nematodes (SCN) and to estimate the suppressive mechanism. Fifteen soils (designated as soil A to O) from different agricultural fields with varying organic inputs were added with SCN-infested soil and grown with a green soybean variety. The SCN density in the soil at 6 weeks of soybean growth was markedly different depending on the soils used, indicating a different level of disease suppressiveness. No significant correlation was observed between the SCN density and any of the soil physicochemical and biological characteristics tested. Then, to estimate a suppression mechanism, F-soil that showed the lowest density of SCN was added to the SCN-infested soil with or without streptomycin to kill bacteria and grown with soybean. SCN density was not increased by the addition of streptomycin, indicating that soil bacteria may not be involved in the suppressiveness of F-soil. In total, 128 fungal strains were isolated from the rhizosphere of F-soil and inoculated in a combination or singly in the SCN-infested soil. After repeated screenings, five strains were selected since the SCN density was consistently decreased by them. Sequence analysis showed that they were closest to Clonostachys rosea, Aspergillus niger, Aspergillus fumigatus, Fusarium oxysporum, and Cylindrodendrum alicantinum. All five strains significantly reduced the mobility of second-stage juveniles (J2). Further, C. rosea a2, A. niger a8, and F. oxysporum a25 significantly decreased hatching. Overall, the present study demonstrated that soil fungi played an important role in SCN suppression in F-soil.

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Section: Discussionmentioning

confidence: 99%

Evaluation of Soil Suppressiveness of Various Japanese Soils against the Soybean Cyst Nematode Heterodera glycines and Its Relation with the Soil Chemical and Biological Properties

Yang,

Wu,

Perry

et al. 2023

Agronomy

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“…Cross-kingdom and cross-species RNA silencing is not only observed in pathogens, but it is quickly being discovered or predicted in a number of biocontrol organisms. For example, Beauveria bassiana can use the milRNA bba-milR1 to attenuate the immune response of its host Anopheles stephensi (a mosquito vector of malaria parasites) (Cui et al, 2019), while many sRNAs of the mycoparasite Clonostachys rosea, another fungal species, were predicted to target virulence factors in Botrytis cinerea and Fusarium graminearum (Piombo et al, 2021(Piombo et al, , 2022. However, the potential for cross-species RNA silencing has never been assessed in biocontrol oomycetes to date.…”

Section: Introductionmentioning

confidence: 99%

RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents

et al. 2023

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IntroductionOomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors.MethodsTo gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species.Results and discussionEach of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5’ base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.

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“…RNA silencing mechanisms have been identified in Phytophthora (Qiao et al, 2013). As discussed by Piombo et al (2023), the form of gene regulation mediated by non-coding small RNAs (sRNAs) is involved in the pathogenicity of the oomycete by transboundary movement of sRNAs or regulation of the expression of effectors. For example, in P. sojae, sRNA regulated transcription of the effector Avr3a, which led to transgenerational silencing (Qiao et al, 2013), while the maintenance of the silenced state of the effector gene Avr1b required H3K27me3 deposition (Wang, Chen, et al, 2020).…”

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confidence: 99%

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology

Guan,

Gajewska,

Floryszak‐Wieczorek

et al. 2024

Molecular Plant Pathology

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Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant‐damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome‐ and proteome‐level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro‐oxidative stress is also briefly discussed.

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Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea

Cited by 7 publications

References 91 publications

Evaluation of Soil Suppressiveness of Various Japanese Soils against the Soybean Cyst Nematode Heterodera glycines and Its Relation with the Soil Chemical and Biological Properties

Evaluation of Soil Suppressiveness of Various Japanese Soils against the Soybean Cyst Nematode Heterodera glycines and Its Relation with the Soil Chemical and Biological Properties

RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology

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