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Department of Plant and Microbial Biology

Publications

  1. Minadakis, N., Jigisha, J., Cornetti, L., Kunz, L., Mueller, M. C., Torriani, S. F., & Menardo, F. (2024). Genomic surveillance and molecular evolution of fungicide resistance in European populations of wheat powdery mildew. bioRxiv, 2024-10. (https://doi.org/10.1101/2024.10.24.619980).
  2. Jigisha, J., Ly, J., Minadakis, N., Freund, F., Kunz, L., Piechota, U., ... & Menardo, F. (2024). Population genomics and molecular epidemiology of wheat powdery mildew in Europe. bioRxiv, 2024-10. (https://doi.org/10.1101/2024.10.24.619980).
  3. Kunz, L., Jigisha, J., Menardo, F., Sotiropoulos, A. G., Zbinden, H., Zou, S., ... & Mueller, M. C. (2024). Avirulence depletion assay: combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew. bioRxiv, 2024-07. (https://doi.org/10.1101/2024.07.10.602895). Accepted, PLoS Pathogens.
  4. Goig, G. A., Menardo, F., Salaam-Dreyer, Z., Dippenaar, A., Streicher, E. M., Daniels, J., ... & Gagneux, S. (2023). Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. The Lancet Microbe, 4(7), e506-e515. (https://doi.org/10.1016/S2666-5247(23)00110-6).
  5. Zwyer, M., Rutaihwa, L. K., Windels, E., Hella, J., Menardo, F., Sasamalo, M., ... & Brites, D. (2023). Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania. PLoS Pathogens, 19(4), e1010893. (https://doi.org/10.1371/journal.ppat.1010893).
  6. Menardo, F. (2022). Understanding drivers of phylogenetic clustering and terminal branch lengths distribution in epidemics of Mycobacterium tuberculosis. Elife, 11, e76780. (https://doi.org/10.7554/eLife.76780).
  7. Walker, T. M., Miotto, P., Köser, C. U., Fowler, P. W., Knaggs, J., Iqbal, Z., ... & Rodwell, T. C. (2022). The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis. Lancet Microbe 3: e265–e273. (https://doi.org/10.1016/S2666-5247(21)00301-3).
  8. Cox, H., Salaam-Dreyer, Z., Goig, G. A., Nicol, M. P., Menardo, F., Dippenaar, A., ... & Reinhard, M. Potential contribution of HIV during first-line tuberculosis treatment to subsequent rifampicin-monoresistant tuberculosis and acquired tuberculosis drug resistance in South Africa: a retrospective molecular epidemiology study. Lancet Microbe 2 (11)(2021) e584–e593. (https://doi.org/10.1016/S2666-5247(21)00144-0).
  9. Salaam-Dreyer, Z., Streicher, E. M., Sirgel, F. A., Menardo, F., Borrell, S., Reinhard, M., ... & Cox, H. (2021). Rifampicin-monoresistant tuberculosis is not the same as multidrug-resistant tuberculosis: A descriptive study from Khayelitsha, South Africa. Antimicrobial Agents and Chemotherapy, 65(11), 10-1128. (https://doi.org/10.1128/aac.00364-21).
  10. Coscolla, M., Gagneux, S., Menardo, F., Loiseau, C., Ruiz-Rodriguez, P., Borrell, S., ... & Brites, D. (2021). Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microbial Genomics, 7(2), 000477. (https://doi.org/10.1099/mgen.0.000477).
  11. Menardo, F., Rutaihwa, L. K., Zwyer, M., Borrell, S., Comas, I., Conceição, E. C., ... & Gagneux, S. (2021). Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000 Research, 10:60 (https://doi.org/10.12688/f1000research.28318.2).
  12. Menardo, F., Gagneux, S., & Freund, F. (2021). Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis. Molecular Biology and Evolution, 38(1), 290-306. (https://doi.org/10.1093/molbev/msaa179).
  13. Ngabonziza, J. C. S., Loiseau, C., Marceau, M., Jouet, A., Menardo, F., Tzfadia, O., ... & Supply, P. (2020). A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nature Communications, 11(1), 2917. (https://doi.org/10.1038/s41467-020-16626-6).
  14. Loiseau, C.*, Menardo, F.*, Aseffa, A., Hailu, E., Gumi, B., Ameni, G., ... & Brites, D. (2020). An African origin for Mycobacterium bovis. Evolution, Medicine, and Public Health, 2020(1), 49-59. (https://doi.org/10.1093/emph/eoaa005). * Equal contribution
  15. Menardo, F., Duchêne, S., Brites, D., & Gagneux, S. (2019). The molecular clock of Mycobacterium tuberculosis. PLoS Pathogens, 15(9), e1008067. (https://doi.org/10.1371/journal.ppat.1008067).
  16. Meehan, C. J., Goig, G. A., Kohl, T. A., Verboven, L., Dippenaar, A., Ezewudo, M., ... & Van Rie, A. (2019). Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology, 17(9), 533-545. (https://doi.org/10.1038/s41579-019-0214-5).
  17. Bourras, S., Kunz, L., Xue, M., Praz, C. R., Müller, M. C., Kälin, C., ... & Keller, B. (2019). The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nature Communications, 10(1), 2292. (https://doi.org/10.1038/s41467-019-10274-1).
  18. Payne, J. L.*, Menardo, F.*, Trauner, A., Borrell, S., Gygli, S. M., Loiseau, C., ... & Hall, A. R. (2019). Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis. PLoS biology, 17(5), e3000265. (https://doi.org/10.1371/journal.pbio.3000265). * Equal contribution
  19. Müller, M. C., Praz, C. R., Sotiropoulos, A. G., Menardo, F., Kunz, L., Schudel, S., ... & Wicker, T. (2019). A chromosome‐scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew. New Phytologist, 221(4), 2176-2189. (https://doi.org/10.1111/nph.15529).
  20. Rutaihwa, L. K., Menardo, F., Stucki, D., Gygli, S. M., Ley, S. D., Malla, B., ... & Gagneux, S. (2019). Multiple introductions of Mycobacterium tuberculosis lineage 2–Beijing into Africa over centuries. Frontiers in Ecology and Evolution, 7, 112. (https://doi.org/10.3389/fevo.2019.00112).
  21. Brites, D., Loiseau, C., Menardo, F., Borrell, S., Boniotti, M. B., Warren, R., ... & Gagneux, S. (2018). A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex. Frontiers in microbiology, 9, 2820. (https://doi.org/10.3389/fmicb.2018.02820).
  22. McNally, K. E., Menardo, F., Lüthi, L., Praz, C. R., Müller, M. C., Kunz, L., ... & Keller, B. (2018). Distinct domains of the AVRPM 3A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. New Phytologist, 218(2), 681-695. (https://doi.org/10.1111/nph.15026).
  23. Praz, C. R., Menardo, F., Robinson, M. D., Müller, M. C., Wicker, T., Bourras, S., & Keller, B. (2018). Non-parent of origin expression of numerous effector genes indicates a role of gene regulation in host adaption of the hybrid triticale powdery mildew pathogen. Frontiers in plant science, 9, 49. (https://doi.org/10.3389/fpls.2018.00049).
  24. Menardo, F., Loiseau, C., Brites, D., Coscolla, M., Gygli, S. M., Rutaihwa, L. K., ... & Gagneux, S. (2018). Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC bioinformatics, 19, 1-8. (https://doi.org/10.1186/s12859-018-2164-8).
  25. Menardo, F., Praz, C. R., Wicker, T., & Keller, B. (2017). Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC evolutionary biology, 17, 1-14. (https://doi.org/10.1186/s12862-017-1064-2).
  26. Zeng, F. S., Menardo, F., Xue, M. F., Zhang, X. J., Gong, S. J., Yang, L. J., ... & Yu, D. Z. (2017). Transcriptome analyses shed new insights into primary metabolism and regulation of Blumeria graminis f. sp. tritici during conidiation. Frontiers in plant science, 8, 1146. (https://doi.org/10.3389/fpls.2017.01146).
  27. Menardo, F., Wicker, T., & Keller, B. (2017). Reconstructing the evolutionary history of powdery mildew lineages (Blumeria graminis) at different evolutionary time scales with NGS data. Genome Biology and Evolution, 9(2), 446-456. (https://doi.org/10.1093/gbe/evx008).
  28. Praz, C. R., Bourras, S., Zeng, F., Sánchez‐Martín, J., Menardo, F., Xue, M., ... & Keller, B. (2017). AvrPm2 encodes an RNase‐like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. New Phytologist, 213(3), 1301-1314. (https://doi.org/10.1111/nph.14372).

  29. Sucher, J.*, Menardo, F.*, Praz, C. R.*, Boni, R., Krattinger, S. G., & Keller, B. (2018). Transcriptional profiling reveals no response of fungal pathogens to the durable, quantitative Lr34 disease resistance gene of wheat. Plant Pathology, 67(4), 792-798. (https://doi.org/10.1111/ppa.12797). * Equal contribution

  30. Menardo, F., Praz, C. R., Wyder, S., Ben-David, R., Bourras, S., Matsumae, H., ... & Keller, B. (2016). Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nature Genetics, 48(2), 201-205. (https://doi.org/10.1038/ng.3485).

  31. Roffler, S., Menardo, F., & Wicker, T. (2015). The making of a genomic parasite-the Mothra family sheds light on the evolution of Helitrons in plants. Mobile DNA, 6, 1-13. (https://doi.org/10.1186/s13100-015-0054-4).

  32. Bourras, S., McNally, K. E., Ben-David, R., Parlange, F., Roffler, S., Praz, C. R., ... & Keller, B. (2015). Multiple avirulence loci and allele-specific effector recognition control the Pm3 race-specific resistance of wheat to powdery mildew. The Plant Cell, 27(10), 2991-3012. (https://doi.org/10.1105/tpc.15.00171).

  33. Parlange, F., Roffler, S., Menardo, F., Ben-David, R., Bourras, S., McNally, K. E., ... & Keller, B. (2015). Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles. Fungal Genetics and Biology, 82, 181-192. (https://doi.org/10.1016/j.fgb.2015.06.009).

  34. Borovec, R.*, Menardo, F.*, & Meregalli, M.* (2013). A new genus of Entiminae from North Africa, supported by a phylogenetic analysis (Coleoptera: Curculionidae: Entiminae). Zoological Journal of the Linnean Society, 167(2), 243-258. (https://doi.org/10.1111/zoj.12001). * Equal contribution

  35.  Meregalli, M., Menardo, F., Klass, K., & Cervella, P. (2013). Phylogeny of the Saxifraga-associated species of Dichotrachelus (Insecta: Coleoptera: Curculionidae), with remarks on their radiation in the Alps. Arthropod Systematics & Phylogeny, 71, 43-68. (https://arthropod-systematics.arphahub.com/article/31765/download/pdf/).

   

Publications at UZH

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Publications

  • 2023

    • Goig, Galo A; Menardo, Fabrizio; Salaam-Dreyer, Zubeida; Dippenaar, Anzaan; Streicher, Elizabeth M; Daniels, Johnny; Reuter, Anja; Borrell, Sonia; Reinhard, Miriam; Doetsch, Anna; Beisel, Christian; Warren, Robin M; Cox, Helen; Gagneux, Sebastien (2023). The Lancet Microbe, 4(7):e506-e515.
    • Zwyer, Michaela; Rutaihwa, Liliana K; Windels, Etthel; Hella, Jerry; Menardo, Fabrizio; Sasamalo, Mohamed; Sommer, Gregor; Schmülling, Lena; Borrell, Sonia; Reinhard, Miriam; Dötsch, Anna; Hiza, Hellen; Stritt, Christoph; Sikalengo, George; Fenner, Lukas; De Jong, Bouke C; Kato-Maeda, Midori; Jugheli, Levan; Ernst, Joel D; Niemann, Stefan; Jeljeli, Leila; Ballif, Marie; Egger, Matthias; Rakotosamimanana, Niaina; Yeboah-Manu, Dorothy; Asare, Prince; Malla, Bijaya; Dou, Horng Yunn; Zetola, Nicolas; Wilkinson, Robert J; et al (2023). PLoS Pathogens, 19(4):e1010893.

  • 2022

    • Menardo, Fabrizio (2022). eLife, 11:e76780.

  • 2021

    • Coscolla, Mireia; Gagneux, Sebastien; Menardo, Fabrizio; Loiseau, Chloé; Ruiz-Rodriguez, Paula; Borrell, Sonia; et al; Fenner, Lukas; Böttger, Erik C (2021). Microbial Genomics, 7(2):1-14.

  • 2019

    • Bourras, Salim; Kunz, Lukas; Xue, Minfeng; Praz, Coraline Rosalie; Müller, Marion Claudia; Kälin, Carol; Schläfli, Michael; Ackermann, Patrick; Flückiger, Simon; Parlange, Francis; Menardo, Fabrizio; Schaefer, Luisa Katharina; Ben-David, Roi; Roffler, Stefan; Oberhaensli, Simone; Widrig, Victoria; Lindner, Stefan; Isaksson, Jonatan; Wicker, Thomas; Yu, Dazhao; Keller, Beat (2019). Nature Communications, 10(1):2292-2308.
    • Müller, Marion C; Praz, Coraline R; Sotiropoulos, Alexandros G; Menardo, Fabrizio; Kunz, Lukas; Schudel, Seraina; Oberhänsli, Simone; Poretti, Manuel; Wehrli, Andreas; Bourras, Salim; Keller, Beat; Wicker, Thomas (2019). New Phytologist, 221(4):2176-2189.

  • 2018

    • McNally, Kaitlin Elyse; Menardo, Fabrizio; Lüthi, Linda; Praz, Coraline Rosalie; Müller, Marion Claudia; Kunz, Lukas; Ben-David, Roi; Chandrasekhar, Kottakota; Dinoor, Amos; Cowger, Christina; Meyers, Emily; Xue, Mingfeng; Zeng, Fangsong; Gong, Shuangjun; Yu, Dazhao; Bourras, Salim; Keller, Beat (2018). New Phytologist, 218(2):681-695.
    • Praz, Coraline R; Menardo, Fabrizio; Robinson, Mark D; Müller, Marion C; Wicker, Thomas; Bourras, Salim; Keller, Beat (2018). Frontiers in Plant Science, 9:49.
    • Sucher, J; Menardo, F; Praz, C R; Boni, R; Krattinger, S G; Keller, B (2018). Plant Biology, 67(4):792-798.

  • 2017

    • Praz, Coraline R; Bourras, Salim; Zeng, Fansong; Sánchez-Martín, Javier; Menardo, Fabrizio; Xue, Minfeng; Yang, Lijun; Roffler, Stefan; Böni, Rainer; Herren, Gerard; McNally, Kaitlin E; Ben-David, Roi; Parlange, Francis; Oberhaensli, Simone; Flückiger, Simon; Schäfer, Luisa K; Wicker, Thomas; Yu, Dazhao; Keller, Beat (2017). New Phytologist, 213(3):1301-1314.
    • Menardo, Fabrizio; Praz, Coraline R; Wicker, Thomas; Keller, Beat (2017). BMC Evolutionary Biology, 17(1):223.
    • Menardo, Fabrizio; Wicker, Thomas; Keller, Beat (2017). Genome Biology and Evolution, 9(2):446-456.

  • 2016

    • Menardo, Fabrizio. 2016, University of Zurich, Faculty of Science.
    • Menardo, Fabrizio; Praz, Coraline R; Wyder, Stefan; Ben-David, Roi; Bourras, Salim; Matsumae, Hiromi; McNally, Kaitlin E; Parlange, Francis; Riba, Andrea; Roffler, Stefan; Schaefer, Luisa K; Shimizu, Kentaro K; Valenti, Luca; Zbinden, Helen; Wicker, Thomas; Keller, Beat (2016). Nature Genetics, 48(2):201-205.

  • 2015

    • Roffler, Stefan; Menardo, Fabrizio; Wicker, Thomas (2015). Mobile DNA:6:23.
    • Parlange, Francis; Roffler, Stefan; Menardo, Fabrizio; Ben-David, Roi; Bourras, Salim; McNally, Kaitlin E; Oberhaensli, Simone; Stirnweis, Daniel; Buchmann, Gabriele; Wicker, Thomas; Keller, Beat (2015). Fungal Genetics and Biology, 82:181-192.
    • Bourras, Salim; McNally, Kaitlin Elyse; Ben-David, Roi; Parlange, Francis; Roffler, Stefan; Praz, Coraline Rosalie; Oberhaensli, Simone; Menardo, Fabrizio; Stirnweis, Daniel; Frenkel, Zeev; Schaefer, Luisa Katharina; Flückiger, Simon; Treier, Georges; Herren, Gerhard; Korol, Abraham B; Wicker, Thomas; Keller, Beat (2015). Plant Cell, 27(10):2991-3012.