LUIGI FAINO

CURRICULUM VITAE LUIGI FAINO

GENERAL INFORMATION

Name: Luigi
Family name: Faino
Sex: Male
Citizenship: Italian
Place and date of birth: Salerno, 21/05/1980
Address: Via Magellano 135, 84098 Pontecagnano Faiano (SA)
Tax code: FNALGU80E21H703E
Tel: +39 3339307158
Email: luigi.faino@uniroma1.it

BIBLIOMETRIC INDEXES AND ASN (source Scopus):
I got the habilitation in AGR/12
Scopus ID-Author = 35344734600
# of Peer review articles = 20
H-index = 12
# of citations = 319

ACADEMIC POSITION

“Ricercatore a Tempo Determianto” (RTDB) Associate Professor in Plant Pathology (scientific-disciplinary sector: AGR/12), Department of Environmental Biology, University of Rome “Sapienza”, Italy.

ACADEMIC RECORDS AND WORKING EXPERIENCE
December 2020-to date: Associate Professor at the Department of Environmental Biology, University of Rome “Sapienza”, Italy.

December 2017-2020: Researcher at the Department of Environmental Biology, University of Rome “Sapienza”, Italy.

August 2016 - November 2017: Researcher in Bioinformatics at Bayer Crop Science – The Netherlands

November 2011 - July 2016: Post-Doc PhD in plant pathology Phytopathology, laboratory of Phytopathology Plant Breeding Department, University of Wageningen (The Netherlands)

November 2006 - November 2011: Post-Doc in Plant Breeding, Laboratory of Plant Breeding, University of Wageningen (The Netherlands)

October 2004 - January 2008: PhD in Plant Biotechnology, University of Naples “Federico II”, Italy

September 1999- October 2004: Degree in Pant Biotechnology, University of Naples “Federico II”, Italy

LINGUISTIC SKILLS

Italian: mother language
English: excellent
Spanish: good

SCIENTIFIC ACTIVITIES

1. Research areas:
• Fungal genomics: key research interest is the study of genome organization and genome evolution of plant pathogenic fungi. Within this area, the main achievement was the completion of the first eukaryotic gapless genome assembly only using Next Generation sequencing technology. Using the genome assembly of Verticillium spp., a genome evolution theory was hypothesized for fungal pathogen without obvious sexual cycle. After the release of the first gapless Verticillium genome, several international collaborations were established aimed to the and genome sequencing project started and more gapless or near complete gnome were generated
• Software and pipelines development: the main objective of this research line is the development of methodology or pipelines to improve genome assembly and annotation of fungal genomes. Fungal genomes are organized differently when compared to other eukaryotic genomes and dedicated tools are required for genome assembly and/or genome annotation. In the last years, several tools and strategy where developed and published.

2. Technical skills
Nucleic acid extraction, PCR, gene expression (real-time PCR, RNA-seq), molecular markers, linkage and association mapping, recombinant DNA technology and genetic transformation, gene silencing, sequencing, field experiment design and conduction; microscopy, pathogenicity trials, fungal genetic transformation, protein extraction and production, plant transformation

3. (Bio)informatics skills
Office, Statistics (R), basic bioinformatics (CLC, Geneious, Primer3), SNP data analysis and Association Mapping (Fluidigm SNP Genotyping, SNP and Variation Suite, TASSEL), Genetic Mapping (JoinMap, MapQTL), gene expression analysis using RNA-seq, Python, Perl, Bash, Phylogenies

4. Referee activities
Reviewer for the following international journals indexed in ISI/Scopus databases: Frontiers in Plant Science.

5. Conferences (oral presentation)
14-04-2014 al 15-04-2014: Third generation sequencing: a magnifying glass to study genomic rearrangements in the fungal plant pathogen Verticillium - ALW NWO Meeting - The Netherlands

08-03-2015 al 08-03-2015: Pathogen genomics; the virtues of finished genomes - MAX Crop Meeting - The Netherlands

26-08-2015 al 28-08-2015: Genome plasticity mediated by transposable elements drives the evolution of virulence in the vascular wilt pathogen Verticillium dahliae. COST meeting - Keil -Germany

21-09-2015 al 23-09-2015: How transposons drive the evolution of fungal pathogen aggressiveness – SIPAV – Torino – Italy

02-09-2016 al 02-09-2016: Genome upgrade and annotation using Nanopore sequencing. Keygene – Wageningen – The Netherlands

05-09-2018 al 07-09-2018: Fungal effector-omics in the genomics “era”: Verticillium and Fusarium study case – SIPAV – Ancona - Italy

DIDACTIC ACTIVITIES

1. BSc and MSc Courses
Academic year 2017-2018/2018-2019: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Physiopathology” within the “Plant and industrial Biotechnology” program (48 hours).

Academic year 2017-2018: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Plant Pathology” within the “Plant and industrial Biotechnology” program (48 hours).

Academic year 2018-2025: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Molecular Plant Pathology” within the “Plant and industrial Biotechnology” program (48 hours).

Academic year 2018-2025: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Bioinformatics in plant pathology” within the “Bioinformatics” program (48 hours).

Academic year 2023-2025: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Principals of bioinformatics" within the “Plant and industrial Biotechnology” program (48 hours).

Academic year 2023-2025: University of Rome “Sapienza”, Rome (Italy), Italy. BSc level course in “Agricultural genetics and Plant Breding” within the BGIA program (48 hours).

2. Tutoring
2009-present: supervision of one PhD students and six MSc students.

ARTICLES

Alassimone, J., Praz, C., Lorrain, C., De Francesco, A., Carrasco-López, C., Faino, L., et al. (2024b) The Zymoseptoria tritici Avirulence Factor AvrStb6 Accumulates in Hyphae Close to Stomata and Triggers a Wheat Defense Response Hindering Fungal Penetration. Molecular Plant-Microbe Interactions® 37: 432–444.
Arcari, G., Di Lella, F.M., Bibbolino, G., Mengoni, F., Beccaccioli, M., Antonelli, G., et al. (2020) A multispecies cluster of VIM-1 carbapenemase-producing enterobacterales linked by a novel, highly conjugative, and broad-host-range IncA plasmid forebodes the reemergence of VIM-1. Antimicrob Agents Chemother 64:.
Beccaccioli, M., Grottoli, A., Scarnati, L., Faino, L., and Reverberi, M. (2021) Nanopore hybrid assembly of biscogniauxia mediterranea isolated from quercus cerris affected by charcoal disease in an endangered coastal wood. Microbiol Resour Announc 10:.
Beccaccioli, M., Moricca, C., Faino, L., Reale, R., Mineo, M., and Reverberi, M. (2023) The Neolithic site “La Marmotta”: DNA metabarcoding to identify the microbial deterioration of waterlogged archeological wood. Front Microbiol 14:.
Bolton, M.D., Ebert, M.K., Faino, L., Rivera-Varas, V., de Jonge, R., Van de Peer, Y., et al. (2016) RNA-sequencing of Cercospora beticola DMI-sensitive and -resistant isolates after treatment with tetraconazole identifies common and contrasting pathway induction. Fungal Genetics and Biology 92: 1–13.
Consoli, S., Caggia, C., Russo, N., Randazzo, C.L., Continella, A., Modica, G., et al. (2023) Sustainable Use of Citrus Waste as Organic Amendment in Orange Orchards. Sustainability 15: 2482.
Cook, D.E., Valle-Inclan, J.E., Pajoro, A., Rovenich, H., Thomma, B.P.H.J., and Faino, L. (2019) Long-read annotation: Automated eukaryotic genome annotation based on long-read cDNA sequencing. Plant Physiol 179:.
Depotter, J.R.L., Shi-Kunne, X., Missonnier, H., Liu, T., Faino, L., van den Berg, G.C.M., et al. (2019) Dynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation. Mol Ecol 28: 3482–3495.
Derbyshire, M., Denton-Giles, M., Hegedus, D., Seifbarghi, S., Rollins, J., Kan, J. Van, et al. (2017) The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol 9: 593–618.
Faino, L., Azizinia, S., Hassanzadeh, B.H., Verzaux, E., Ercolano, M.R., Visser, R.G.F., and Bai, Y. (2012) Fine mapping of two major QTLs conferring resistance to powdery mildew in tomato. Euphytica 184: 223–234.
Faino, L., Carli, P., Testa, A., Cristinzio, G., Frusciante, L., and Ercolano, M.R. (2010) Potato R1 resistance gene confers resistance against Phytophthora infestans in transgenic tomato plants. Eur J Plant Pathol 128: 233–241.
Faino, L., de Jonge, R., and Thomma, B.P.H.J. (2012) The transcriptome of Verticillium dahliae-infected Nicotiana benthamiana determined by deep RNA sequencing. Plant Signal Behav 7: 1065–1069.
Faino, L., Scala, V., Albanese, A., Modesti, V., Grottoli, A., Pucci, N., et al. (2021) Nanopore sequencing for the detection and identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material. Plant Pathol.
Faino, L., Seidl, M.F., Datema, E., Van Den Berg, G.C.M., Janssen, A., Wittenberg, A.H.J., and Thomma, B.P.H.J. (2015) Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome. mBio 6:.
Faino, L., Seidl, M.F., Shi-Kunne, X., Pauper, M., Van Den Berg, G.C.M., Wittenberg, A.H.J., and Thomma, B.P.H.J. (2016) Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res 26: 1091–1100.
Faino, L. and Thomma, B.P.H.J. (2014) Get your high-quality low-cost genome sequence. Trends Plant Sci 19: 288–291.
Van Kan, J.A.L., Stassen, J.H.M., Mosbach, A., Van Der Lee, T.A.J., Faino, L., Farmer, A.D., et al. (2017) A gapless genome sequence of the fungus Botrytis cinerea. Mol Plant Pathol 18: 75–89.
Kratter, M., Beccaccioli, M., Vassallo, Y., Benedetti, F., La Penna, G., Proietti, A., et al. (2024) Long-term monitoring of the hypogeal Etruscan Tomba degli Scudi, Tarquinia, Italy. Early detection of black spots, investigation of fungal community, and evaluation of their biodeterioration potential. J Appl Microbiol 135:.
Li, C., Faino, L., Dong, L., Fan, J., Kiss, L., de Giovanni, C., et al. (2012) Characterization of polygenic resistance to powdery mildew in tomato at cytological, biochemical and gene expression level. Mol Plant Pathol 13: 148–159.
Sanseverino, W., Roma, G., De Simone, M., Faino, L., Melito, S., Stupka, E., et al. (2009) PRGdb: A bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res 38:.
Santhanam, P., Van Esse, H.P., Albert, I., Faino, L., Nürnberger, T., and Thomma, B.P.H.J. (2013) Evidence for functional diversification within a fungal Nep1-like protein family. Molecular Plant-Microbe Interactions 26: 278–286.
Scala, V., Faino, L., Costantini, F., Crosara, V., Albanese, A., Pucci, N., et al. (2023) Analysis of Italian isolates of Pantoea stewartii subsp. stewartii and development of a real-time PCR-based diagnostic method. Front Microbiol 14:.
Seidl, M.F., Faino, L., Shi-Kunne, X., Van Den Berg, G.C.M., Bolton, M.D., and Thomma, B.P.H.J. (2015) The genome of the saprophytic fungus Verticillium tricorpus reveals a complex effector repertoire resembling that of its pathogenic relatives. Molecular Plant-Microbe Interactions 28: 362–373.
Seidl, M.F., Kramer, H.M., Cook, D.E., Fiorin, G.L., van den Berg, G.C.M., Faino, L., and Thomma, B.P.H.J. (2020) Repetitive elements contribute to the diversity and evolution of centromeres in the fungal genus verticillium. mBio 11: 1–22.
Seifi, A., Gao, D., Zheng, Z., Pavan, S., Faino, L., Visser, R.G.F., et al. (2014) Genetics and molecular mechanisms of resistance to powdery mildews in tomato (Solanum lycopersicum) and its wild relatives. Eur J Plant Pathol 138: 641–665.
Severing, E., Faino, L., Jamge, S., Busscher, M., Kuijer-Zhang, Y., Bellinazzo, F., et al. (2018) Arabidopsis thaliana ambient temperature responsive lncRNAs. BMC Plant Biol 18:.
Shi-Kunne, X., Faino, L., van den Berg, G.C.M., Thomma, B.P.H.J., and Seidl, M.F. (2018) Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol 20: 1362–1373.
Shi-Kunne, X., Seidl, M.F., Faino, L., and Thomma, B.P.H.J. (2015) Draft genome sequence of a strain of cosmopolitan fungus Trichoderma atroviride. Genome Announc 3: e00287-15.
Snelders, N.C., Boshoven, J.C., Song, Y., Schmitz, N., Fiorin, G.L., Rovenich, H., van den Berg, Grardy C. M., et al. (2022) A highly polymorphic effector protein promotes fungal virulence through suppression of plant‐associated Actinobacteria. New Phytologist.
Thomma, B.P.H.J., Seidl, M.F., Shi-Kunne, X., Cook, D.E., Bolton, M.D., van Kan, J.A.L., and Faino, L. (2016) Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genetics and Biology 90: 24–30.
Turco, S., Grottoli, A., Drais, M.I., De Spirito, C., Faino, L., Reverberi, M., et al. (2021) Draft Genome Sequence of a New Fusarium Isolate Belonging to Fusarium tricinctum Species Complex Collected From Hazelnut in Central Italy. Front Plant Sci 12:.
Valero-Jiménez, C.A., Faino, L., Spring in’t Veld, D., Smit, S., Zwaan, B.J., and van Kan, J.A.L. (2016) Comparative genomics of Beauveria bassiana: Uncovering signatures of virulence against mosquitoes. BMC Genomics 17: 986.
Wolters, P.J., Faino, L., Van Den Bosch, T.B.M., Evenhuis, B., Visser, R.G.F., Seidl, M.F., and Vleeshouwers, V.G.A.A. (2018) Gapless genome assembly of the potato and tomato early blight pathogen alternaria solani. Molecular Plant-Microbe Interactions 31: 692–694.