VIRUS-FUNGUS-PLANT INTERACTION

Group leader: María A. Ayllón - Associate Professor
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Personnel:

 

Research description:

Fungal pathogens induce a variety of diseases in both plants and post-harvest food crops, resulting in significant crop losses for the agricultural industry and becoming in major threats to global food security. Chemical fungicides are commonly used to control fungal diseases, but they have negative impacts to the environment and human health. The Green Deal of the EU has set a goal of reduction in pesticide use by 50% in 2030, in order to move towards a more environmentally-friendly and lower health risk modern agriculture. One safe and eco-friendly alternative to control fungal diseases could be the use of mycoviruses that induce hypovirulence in their fungal hosts.

The long term research goal of the “Virus-Fungus-Plant Interaction” group is to understand the molecular mechanisms of the interaction of mycoviruses with plant pathogenic fungi, and the effects of this interaction on fungus pathogenicity and virulence in plants. For this, we seek to understand the diversity and evolution of mycoviruses, which will lead to explore different life-styles in terms of virus-fungus interactions. Ultimately, our research may provide biological and biotechnological tools based in natural or synthetic mycoviruses for the biocontrol of plant pathogenic fungi. The group works with different biological systems, however, the main model system studied is the necrotrophic ascomycete fungus Botrytis cinerea and its different mycoviruses.

 

The main research lines of the group are focused on:


1. Diversity and evolution of mycoviruses

Discovery and molecular characterization of novel mycoviruses infecting plant pathogenic fungi; evolutional history and evolutionary relationships of unique mycoviruses with known viruses.

Our group has made relevant contributions to the identification and molecular characterization of novel mycoviruses in different genera of fungi and oomycetes. Major findings indicate novel life-cycles on the basis of mycoviruses genomic structures. Current research focuses mainly on multisegmented single-stranded RNA and DNA mycoviruses (Figure 1). On this field, we are actively collaborating with the International Committee on Taxonomy of Viruses in Study Groups of several viral families as Botourmiaviridae family (Figure 2).

 

 

Figure 1. Schematic representation of Botrytis cinerea bocivirus 1 (BcBV1) vcRNA (viral RNA complementary strand) segments showing the locations of ORFs, alignment of the conserved sequences of the 5’ and 3’ ends of BcBV1 RNA1, -2, and -3, and the panhandle structures formed by the 5’ and 3’ termini of each RNA segment (Ruiz-Padilla et al. 2021).

 

Figure 2. Evolutionary relationships of the family Botourmiaviridae and narna-like viruses (Ayllón and Vainio, 2023).

 


2. Molecular mechanisms underlying fungal responses to mycoviral infections

Characterization of the requirements of different mycoviral life cycle steps and the interaction at molecular level with its fungal host, using natural mycoviruses or mycoviral reverse genetic systems. Determination of the molecular mechanisms involved in the plant response to infection by mycovirus-infected fungi.

Our group has contributed to the knowledge of mycovirus effect on fungal infection, showing different alterations that imply virulence reductions of the fungus in planta. Our group has also contributed to the knowledge of B. cinerea RNA silencing machinery as a defense mechanism against mycoviral infection (Figure 3), which has allowed the selection of mycoviruses with efficient replication under fungal silencing.




Figure 3. Size distribution of mycovirus-derived small RNAs (vsiRNAs). Histograms show the percentage of each size length of total reads (top) and unique sequences (bottom) from mycovirus-derived sRNAs sequenced in the three fungal isolates (Donaire and Ayllón, 2017).

 


3. Development of natural biological control agents based in mycoviruses and construction of synthetic mycoviruses

Biological characterization of mycoviruses causing a decrease of the fungal virulence on the plant (hypovirulence) and evaluation of their potential as biocontrol agents. Construction of infectious clones based on cryptic mycoviruses for the development of synthetic mycoviruses.


Our group has characterized the mycovirome of a set of more than 400 field isolates collection of B. cinerea (Figure 4). Some of the molecular characterized mycoviruses have been already described to induce hypovirulence in Botrytis spp. or other fungi., The group explores new biological strategies to control plant fungal diseases using fungal isolates with hypovirulence mediated by mycoviral infection. Currently, we are assessing the potential of several infected fungal strains as biological control agents of B. cinerea.


We also have a wide experience on the generation and manipulation of infectious clones of the most complex plant viruses. On this way, our group developed single-stranded positive sense RNA mycoviruses infectious clones for the future construction of synthetic mycoviruses (Figure 5). We aim to perform functional studies of mycovirus-fungus interaction and to explore new biotechnological strategies to control plant fungal diseases.

 


Figure 4. Phenotype diversity in a B. cinerea field collection.

 

      

 

Figure 5. Schematic representation of the construction of the infectious Botrytis virus F (BVF). Virulence of virus-free and BVF-488–transfected B. cinerea isolates B05.10 and Pi258.9. Comparison of mean lesion area (cm2) at 72 h after inoculation with mycelial agar plugs on detached tomato leaves and pepper leaves of (A) B05.10 and (B) Pi258.9 strains (Córdoba et al. 2022).

 


Competitive research grants:

  1. Molecular mechanism involved in the interaction of Botrytis cinerea-host plant mediated by a mycoviral infection. Ministerio de Ciencia e Innovación PID2020-120106RB-I00. 2021-2024. PI: María A. Ayllón and Julio L. Rodríguez-Romero
    https://twitter.com/
  2. Virome NGS analysis of pests and pathogens for plant protection. H2020-SFS-17, 2018-2021. PI: María A. Ayllón
    https://www.viroplant.eu/
    https://www.instagram.com/viroplant/?hl=es
    https://www.youtube.com/channel/UCTTQ45Ay9Th-vpaEqp_r7OQ
    https://twitter.com/viroplanth2020


Representative Publications

Donaire, L., Xie, J., Nerva, L., Jiang, D., Marzano, S.-Y.L., Sabanadzovic, S., Turina, M., Ayllón, M.A. 2024. ICTV Virus Taxonomy Profile: Botourmiaviridae 2024. Journal of General Virology 105, 002047. DOI: 10.1099/jgv.0.002047

Muñoz-Suárez, H., Ruiz-Padilla, A., Donaire, L., Benito, E.P., Ayllón, M.A. 2024. Reexamining the Mycovirome of Botrytis spp.. Viruses 16. DOI: 10.3390/v16101640

Khalifa, M.E., Ayllón, M.A., Rodriguez Coy, L., Plummer, K.M., Gendall, A.R., Chooi, K.M., van Kan, J.A.L., MacDiarmid, R.M. 2024. Mycologists and Virologists Align: Proposing Botrytis cinerea for Global Mycovirus Studies. Viruses 16, 1483. DOI: 10.3390/v16091483

Chiba, S., Suzuki, N., Velasco, L., Ayllón, M.A., Lee-Marzano, S.-Y., Sun, L., Sabanadzovic, S., Turina, M. 2024. ICTV Virus Taxonomy Profile: Fusariviridae 2024. Journal of General Virology 105, 001973. DOI: 10.1099/jgv.0.001973

Córdoba, L., Ruiz-Padilla, A., Pardo-Medina, J., Rodríguez-Romero, J.L., Ayllón, M.A. 2024. Construction of a Mycoviral Infectious Clone for Reverse Genetics in Botrytis cinerea, in: Medina, C., López-Baena, F.J. (Eds.), Host-Pathogen Interactions: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 47–68. DOI: 10.1007/978-1-0716-3617-6_4

Ruiz-Padilla, A., Rodríguez-Romero, J.L., Pacifico, D., Chiapello, M., Ayllón, M.A. 2024. Determination of the Mycovirome of a Necrotrophic Fungus, in: Pantaleo, V., Miozzi, L. (Eds.), Viral Metagenomics: Methods and Protocols, Methods in Molecular Biology. Springer US, New York, NY, pp. 83–101. DOI: 10.1007/978-1-0716-3515-5_6

Kuhn, J.H., Abe, J., Adkins, S., Alkhovsky, S.V., Avšič-Županc, T., Ayllón, M.A., 2023. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). Journal of General Virology 104, 001864. DOI: 10.1099/jgv.0.001864

Chiba, S., Velasco, L., Ayllón, M.A., Suzuki, N., Lee-Marzano, S.-Y., Sun, L., Sabanadzovic, S., Turina, M. 2023. ICTV Virus Taxonomy Profile: Hypoviridae 2023. Journal of General Virology 104, 001848. DOI: 10.1099/jgv.0.001848

Ayllón, M.A., Vainio, E.J. 2023. Chapter One - Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle, in: Kielian, M., Roossinck, M.J. (Eds.), Advances in Virus Research. Academic Press, pp. 1–86. DOI: 10.1016/bs.aivir.2023.02.002

Ruiz-Padilla, A., Turina, M., Ayllón, M.A. 2023. Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide. Virology Journal 20, 306. DOI: 10.1186/s12985-023-02256-z

Kuhn, J.H., Adkins, S., Alkhovsky, S.V., Avšič-Županc, T., Ayllón, M.A., et al. 20222022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology 167, 2857–2906. DOI: 10.1007/s00705-022-05546-z

Wagemans, J., Holtappels, D., Vainio, E., Rabiey, M., Marzachì, C., Herrero, S., Ravanbakhsh, M., Tebbe, C.C., Ogliastro, M., Ayllón, M.A., Turina, M. 2022. Going Viral: Virus-Based Biological Control Agents for Plant Protection. Annual Review of Phytopathology 60, 21–42. DOI: 10.1146/annurev-phyto-021621-114208

Jiāng, D., Ayllón, M.A., Marzano, S.-Y.L., Kondō, H., Turina, M., ICTV Report ConsortiumYR 2022. ICTV Virus Taxonomy Profile: Mymonaviridae 2022. Journal of General Virology 103, 001787. DOI: 10.1099/jgv.0.001787

Forgia, M., Chiapello, M., Daghino, S., Pacifico, D., Crucitti, D., Oliva, D., Ayllon, MA., Turina, M. 2022 Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris. Virus Evolution 8, veac038. DOI: 10.1093/ve/veac038

Galán-Cubero, R., Córdoba, L., Rodríguez-Romero, J., Chiapello, M., Turina, M., Ayllón, M.A. 2022. Molecular Data of a Novel Penoulivirus Associated with the Plant-Pathogenic Fungus Erysiphe necator. Phytopathology® PHYTO-12-21-0536-A. DOI: 10.1094/PHYTO-12-21-0536-A

Córdoba, L., Ruiz-Padilla, A., Rodríguez-Romero, J., Ayllón, M.A. 2022. Construction and Characterization of a Botrytis Virus F Infectious Clone. Journal of Fungi 8, 459. DOI: 10.3390/jof8050459

Kuhn, J.H., Adkins, S., Agwanda, B.R., Al Kubrusli, R., Alkhovsky, S.V., Amarasinghe, G.K., Avšič-Županc, T., Ayllón, M.A.et al. 2021. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology 166, 3567–3579. DOI: 10.1007/s00705-021-05266-w

Kuhn, J.H., Adkins, S., Agwanda, B.R., Al Kubrusli, R., Alkhovsky, S.V., Amarasinghe, G.K., Avšič-Županc, T., Ayllón, M.A. et al. 2021. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology 166, 3513–3566. DOI: 10.1007/s00705-021-05143-6

Ruiz-Padilla, A., Rodríguez-Romero, J., Gómez-Cid, I., Pacifico, D., Ayllón, M.A. 2021. Novel Mycoviruses Discovered in the Mycovirome of a Necrotrophic Fungus. mBio 12. DOI: 10.1128/mBio.03705-20

Chiapello, M., Rodríguez-Romero, J., Ayllón, M.A., Turina, M. 2020. Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages. Virus Evolution 6. DOI: 10.1093/ve/veaa058

Kuhn, J.H., Adkins, S., Alioto, D., Alkhovsky, S.V., Amarasinghe, G.K., Anthony, S.J., Avšič-Županc, T., Ayllón, M.A., et al. 2020. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Archives of Virology. DOI: 10.1007/s00705-020-04731-2

Ayllón, M.A., Turina, M., Xie, J., Nerva, L., Marzano, S.-Y.L., Donaire, L., Jiang, D., Consortium, I.R. 2020. ICTV Virus Taxonomy Profile: Botourmiaviridae. Journal of General Virology. DOI: 10.1099/jgv.0.001409

Chiapello, M., Rodríguez‐Romero, J., Nerva, L., Forgia, M., Chitarra, W., Ayllón, M.A., Turina, M. 2020. Putative new plant viruses associated with Plasmopara viticola-infected grapevine samples. Annals of Applied Biology. DOI: 10.1111/aab.12563

Jiāng (姜道宏), D., Ayllón, M.A., Marzano, S.-Y.L., ICTV Report Consortium 2019. ICTV Virus Taxonomy Profile: Mymonaviridae. Journal of General Virology. DOI: 10.1099/jgv.0.001301

Amarasinghe, G.K., Ayllón, M.A., et al. 2019. Taxonomy of the order Mononegavirales: update 2019. Archives of Virology. DOI: 10.1007/s00705-019-04247-4

Maes, P., Amarasinghe, G.K., Ayllón, M.A., et al. 2019. Taxonomy of the order Mononegavirales: second update 2018. Archives of Virology. DOI: 10.1007/s00705-018-04126-4

Parizad, S; Dizadji, A; Koohi Habibi, M; Winter, S; Kalantari, S; Movi, S; García-Arenal, F; Ayllón, MA. 2018. "Description and genetic variation of a distinct species of Potyvirus infecting saffron (Crocus sativus L.) plants in major production regions in Iran". Annals of Applied Biology 2018 v.173 no.3 pp. 233-242. DOI: 10.1111/aab.12456".

Fernández-Tabanera, E; Fraile, A; Lunello, P; Garcia-Arenal, F; Ayllon, MA. 2018. "First Report of Onion Yellow Dwarf Virus in Leek (Allium ampeloprasum var. porrum) in Spain". Plant Disease. DOI: 10.1094/PDIS-06-17-0892-PDN".

Parizad, S; Dizadji, A; Koohi Habibi, M; Winter, S; Kalantari, S; Garcia-Arenal, F; Ayllón, MA. 2017. "Prevalence of saffron latent virus (saLV), a new Potyvirus species, in saffron fields of Iran". Journal of Plant Pathology. DOI: 10.4454/jpp.v99i3.3963".

Illana, A; Marconi, M; Rodríguez-Romero, J; Xu, P; Dalmay, T; Wilkinson, MD; Ayllón, MÁ; Sesma, A. 2017. "Molecular characterization of a novel ssRNA ourmia-like virus from the rice blast fungus Magnaporthe oryzae". Archives of Virology. DOI: 10.1007/s00705-016-3144-9".

Donaire, L; Ayllón, MA. 2017. "Deep sequencing of mycovirus-derived small RNAs from Botrytis species". Molecular Plant Pathology. 18(8): 1127-1137. DOI: 10.1111/mpp.12466".

Donaire, L; Pagán, I; Ayllón, MA. 2016. "Characterization of Botrytis cinerea negative-stranded RNA virus 1, a new mycovirus related to plant viruses, and a reconstruction of host pattern evolution in negative-sense ssRNA viruses". Virology. DOI: http://dx.doi.org/10.1016/j.virol.2016.09.017".

Donaire, L; Rozas, J; Ayllón, MA. 2016. "Molecular characterization of Botrytis ourmia-like virus, a mycovirus close to the plant pathogenic genus Ourmiavirus". Virology. DOI: 10.1016/j.virol.2015.11.027".

Rodríguez-García, C; Medina, V; Alonso, A; Ayllón, MA. 2014. "Mycoviruses of Botrytis cinerea isolates from different hosts". Annals of Applied Biology. DOI: 10.1111/aab.12073".