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Edoardo Piombo

Edoardo Piombo
I am a bioinformatician skilled in data mining and visualization. I have experience in working with high-throughput sequencing data coming from genome, transcriptome or metagenome sequencing, with a focus on plant pathology.


After completing my PhD at the University of Turin in April 2020, I started working as a postdoc at slu in August 2020, performing data analysis for the group of Agricultural Plant Pathology ( at the department of Forse Mycology and Plant Pathology ( The focus of my research is the role of small RNAs in the biocontrol activity of the fungus Clonostachys rosea.


At the University of Turin:

Practical and theoretical lessons in bioinformatics and data analysis to bachelor and master students

Practical lessons about RNA extractions to master students



Practical lessons for master students (SLU Advanced Plant Pathology course, 2022)

Practical and theoretical lessons for PhD students (NOVA course 2021 and 2022)

PhD course organization (Navigating large biological datasets with simple bioinformatics tools, 2023)



At the University of Turin the focus of my activity was the Fusarium fujikuroi-rice pathosystem, which I studied mainly through comparative genomics approaches using F. fujikuroi strains with different phenotypes. Apart from bioinformatic analysis, I also conducted RNA extractions and quantitiative RT-PCRs to analyze the gene expression of genes of interest, as well as monitoring the symptoms of rice plants in greenhouse and climate chambers. I was also involved in a number of secondary projects, including secondary metabolite cluster analysis in Penicillium spp., promoter analysis to look for transcription factor binding sites on Penicillium griseofulvum, metagenomic analysis of dates and apples and genome assembly and annotation in Metschnikowia fructicola.

My PhD supervisor was Professor Davide Spadaro (


At SLU I am mainly studying the role of small RNAs (sRNAs) in the biocontrol activity of the fungus Clonostachys rosea. To do this I analyze transcriptome and sRNA sequencing data in C. rosea interacting with pathogens such as Botrytis cinerea and Fusarium graminearum, and I look for sRNA putatively able to affect the expression of C. rosea genes involved in biocontrol. Moreover, I look for sRNAs able to move to the pathogen organisms and affect their gene regulation directly, in what is knows as cross-species RNA silencing.

Apart from this, I give my group support on a variety of bioinformatic operations, including transcriptome analysis, metabarcoding, genome assembly, gene prediction and annotation and generic data mining.

My current supervisor is Professor Magnus Karlsson (


During my PhD studies I had two visiting periods in host institutions.

The first one was at the Centre for Genomic Regulations of Barcelona, supervised by Toni Gabaldón. Here I worked mostly on secondary metabolism prediction and comparison in Penicillium spp.

The second one was at the Volcani Center in Israel (supervisor: Samir Droby). Here I worked on metabarcoding and metagenomics analyses on the microbiome of dates and apples.



Bachelor degree in Biotechnologies, University of Turin, 2011-2014

Master degree in Plant Biotechnologies, University of Turin, 2014-2016.

During my master studies  I was in a three months Erasmus visit at the Université catholique de Louvain, where I conducted an internship supervised by Professor Claude Bragard.

Selected publications

·        Piombo, E., Vetukuri, R. R., Sundararajan, P., Kushwaha, S., Jensen, D. F., Karlsson, M. and Dubey, M. (2022). Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea. Applied and Environmental Microbiology, 88, 13.

·        Piombo, E., Vetukuri, R.R., Broberg, A., Kalyandurg, P.B., Kushwaha, S., Jensen, D.F., Karlsson, M. and Dubey, M. (2021) Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. Microbiology Spectrum, 9, e01099-21.

·        Piombo, E. and Dubey, M (2022) Computational analysis of HTS data and its application in plant pathology. In Plant Pathology (pp. 275-307). Humana, New York, NY

·        Piombo, E., Rosati, M., Sanna, M., Mezzalama, M., Gullino, M. L. and Spadaro, D. (2021). Sequencing of non-virulent strains of Fusarium fujikuroi reveals genes putatively involved in bakanae disease of rice. Fungal Genetics and Biology, 103622.
·        Piombo, E., Abdelfattah, A., Droby, S., Wisniewski, M., Spadaro, D. and Schena, L. (2021). Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms, 9, 188.

·        Piombo, E., Abdelfattah, A., Danino, Y., Salim, S., Feygenberg, O., Spadaro, D., Wisniewski, M. and Droby, S. (2020). Characterizing the Fungal Microbiome in Date (Phoenix dactylifera) Fruit Pulp and Peel from Early Development to Harvest. Microorganisms, 8, 641.

·        Piombo, E., Bosio, P., Acquadro, A., Abbruscato, P. and Spadaro, D. (2020). Different phenotypes, similar genomes: three newly sequenced Fusarium fujikuroi strains induce different symptoms in rice depending on temperature. Phytopathology, 110, 656-665.

·        Piombo, E., Sela, N., Wisniewski, M., Hoffmann, M., Gullino, M. L., Allard, M. W., Levin, E., Spadaro, D. and Droby, S. (2018). Genome sequence, assembly and characterization of two Metschnikowia fructicola strains used as biocontrol agents of postharvest diseases. Frontiers in Microbiology, 9, 593.

·        Aragona, M., Campos-Soriano, L., Piombo, E., Romano, E., San Segundo, B., Spadaro, D. and Infantino, A. (2021). Imaging the invasion of rice roots by the bakanae agent Fusarium fujikuroi using a GFP-tagged isolate. European Journal of Plant Pathology, 1-12.

·        Berihu, M., Somera T. S., Malik, A., Medina, S., Piombo, E., Tal, S., Cohen, M., Ginatt, A., Ofek‑Lalzar, M., Doron‑Faigenboim, A., Mazzola, M., and Freilich, S. (2023). A framework for the targeted recruitment of crop‑beneficial soil taxa based on network analysis of metagenomics data. Microbiome, 11(1), 8.

·        Garello, M., Piombo, E., Prencipe, S., Schiavon, G., Berra, L., Wisniewski, M., Droby, S., and Spadaro, D. (2023). Fruit microbiome: A powerful tool to study the epidemiology of dry lenticel rot and white haze–Emerging postharvest diseases of apple. Postharvest Biology and Technology, 196, 112163.

·        Spadaro, D., Fontana, M., Prencipe, S., Valente, S., Piombo, E. and Gullino, M.L. (2021). Innovative Strategies for the Management of Aspergillus spp. and Penicillium spp. on Nuts. In Postharvest Pathology (pp. 111-127). Springer, Cham.

·        Valente, S., Piombo, E., Schroeckh, V., Meloni, G. R., Heinekamp, T., Brakhage, A. A. and Spadaro, D. (2021). CRISPR-Cas9-Based Discovery of the Verrucosidin Biosynthesis Gene Cluster in Penicillium polonicum. Frontiers in microbiology, 12, 1114.

·        Sui, Y., Wisniewski, M., Droby, S., Piombo, E., Wu, X. and Yue, J. (2020). Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Frontiers in Microbiology, 11, 295.

·        Valente, S., Cometto, A., Piombo, E., Meloni, G. R., Ballester, A. R., González-Candelas, L. and Spadaro, D. (2020). Elaborated regulation of griseofulvin biosynthesis in Penicillium griseofulvum and its role on conidiation and virulence. International Journal of Food Microbiology, 328, 108687.


Visiting Research Fellow at the Department of Forest Mycology and Plant Pathology; Division of Plant Pathology
Postal address:
Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA
Visiting address: Almas Allé 5, Uppsala