Emanuele De Paoli. Research Scientist and Assistant Professor Department of Agricultural and Environmental Sciences University of Udine

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1 Curriculum Vitae Last update July 1 st 2014 Emanuele De Paoli Research Scientist and Assistant Professor Department of Agricultural and Environmental Sciences University of Udine Phone: AREA OF EXPERTISE Plant genomics, epigenomics and bioinformatics PROFESSIONAL EXPERIENCE 2011-present Assistant Professor at the University of Udine (Italy) Keywords: DNA methylation analysis, Epigenomics of Arabidopsis and fruit crops. In my current position at the University of Udine, I am pursuing my research interests in plant genetics with emphasis on epigenomics. I collaborate with the research group of Prof. Michele Morgante from the University of Udine and Prof. Mario Pezzotti from the University of Verona for the analysis of DNA methylation in grapevine focusing on the role of epigenetics in genotype by environment interactions. I also started collaborating with the Istituto di Genomica Applicata (IGA; where I am responsible for organizing the sequencing and analysis of plant DNA methylomes within the Italian Epigenomics Flagship Project EPIGEN, an Italian network for the study of epigenetics in different species (www.epigen.it). In 2012 I was awarded a PRIN grant (Research Programs of Relevant National Interest) by the Italian Ministry of Education, University and Research within the project The control of plant root growth: a systems biology approach coordinated by Prof. Paolo Costantino from the University of Rome Università La Sapienza. I currently teach the course of General Genetics to bachelor students of the Biotechnology curriculum at the University of Udine and I have a participation in the course of Genome Analysis and Bioinformatics organized by Prof. Michele Morgante for master students of the Crop Sciences curriculum. Starting from 2014, I am also faculty member of the PhD program in Molecular Biology of SISSA - Scuola Internazionale Superiore di Studi Avanzati, Trieste. Since January 2014 I am visiting scientist in Prof. Vincent Colot's laboratory at the Istitut de Biologie de l'école normale supérieure (IBENS) in Paris, where I am responsible for conducting research on processes of whole genome DNA methylation recovery. 1

2 Postdoctoral Researcher in Dr. Azeddine Si-Ammour lab. Istituto Agrario di San Michele all Adige (IASMA) and Fondazione Edmund Mach (FEM). Keywords: Small RNAs, RNA degradome, gene silencing, high-throughput sequencing. As a senior postdoc in the research group of Dr. Azeddine Si-Ammour for a short time between 2010 and 2011 I focused on the analysis of gene expression and posttranscriptional silencing in the fruit crops grapevine and apple and contributed to the characterization of grapevine small RNA biogenesis mutants Postdoctoral Researcher in Prof. Pamela J. Green and Prof. Blake C. Meyers s labs. University of Delaware & Delaware Biotechnology Institute. Keywords: Small RNAs, RNA degradome, gene silencing, high-throughput sequencing. I was employed as a postdoctoral researcher by the University of Delaware (USA) to work in Prof. Pamela J. Green s laboratory in the Department of Plant and Soil Sciences and Delaware Biotechnology Institute. I was the principle responsible to carry out the project Deep Sequencing of Plant Small RNAs supported by the National Science Foundation Grant # (to Pamela J. Green and Blake C. Meyers; see also As such, I was in charge of planning and organizing the high-throughput sequencing of small RNA libraries from several different plant samples in collaboration with Illumina. Moreover I conducted computational analyses of small RNA sequencing data from more than 30 plant species in collaboration with Prof. Blake Meyers s laboratory at the Delaware Biotechnology Institute and Prof. Stefan de Folter s group at LANGEBIO Postdoctoral Researcher in Prof. Michele Morgante s lab. University of Udine (Italy). Keywords: BAC sequencing, genomic annotation, transposable elements. I extended my research within the Norway spruce genomic project initiated during the Ph.D., focusing in particular on the annotation and characterization of repetitive elements in Norway spruce. I also collaborated with other labs at the University of Udine, especially for bioinformatic analyses in plant molecular taxonomy Research Assistant in Prof. Michele Morgante s lab. University of Udine (Italy). Keywords: Genetic diversity, linkage disequilibrium, BAC sequencing, genomic annotation. As a Ph.D. student, I was in charge of conducting a survey of genetic diversity and linkage disequilibrium in conifers within the EU project TREESNIPS as well as characterizing the Norway spruce genome by the sequencing and annotation of large genomic regions. 2

3 Teaching Assistant at the University of Udine (Italy). I contributed to the teaching of two courses (Fundamentals of Genetics and Fundamentals of Genomics and Quantitative Genetics) for undergraduate students in biotechnology, focusing in particular on the preparation to the final tests. I prepared substitute lectures, counseled and tutored students, and had full responsibility for grading students performance in the class Research Assistant in Prof. Mauro Giacca s lab. International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy. EDUCATION Keywords: DNA methylation, gene expression, gene therapy, retrovirus As an undergraduate research assistant, I planned and conducted experiments with my advisors to examine both expression pattern and methylation status of a myelotropic-specific retroviral vector designed for gene therapy purposes Ph.D. - Biotechnological Sciences - University of Udine (Italy). Advisor: Prof. Michele Morgante. Dissertation: Genetic diversity, linkage disequilibrium and repetitive component of the genome in Norway spruce [Picea abies L. (K.)] year-degree in Biological Sciences - University of Trieste (Italy). Final evaluation: 110/110 cum laude. Advisors: Prof. Mauro Giacca and Dr. Riccardo Priore International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy. Thesis: Expression pattern and methylation analysis of a myelotropic-specific retroviral vector for gene therapy. PUBLICATIONS Montes RA*, de Fátima Rosas-Cárdenas F*, De Paoli E*, Accerbi M, Rymarquis LA, Mahalingam G, Marsch-Martínez N, Meyers BC, Green PJ, de Folter S (2014). Sample sequencing of vascular plants demonstrates widespread conservation and divergence of micrornas. NATURE COMMUNICATIONS Apr 23;5:3722. doi: /ncomms4722. *equally contributed Larsson H, De Paoli E, Morgante M, Lascoux M, Gyllenstrand N (2013). The Hypomethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies). TREE GENETICS & GENOMES, 9: , ISSN: Prezza N, Del Fabbro C, Vezzi F, De Paoli E, Polocriti A (2012). ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet. PROCEEDINGS OF THE 2012 ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata 3

4 D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, Xu X, Pan S, Cheng S, Liu X, Ren Y, Wang J, Albiero A, Dal Pero F, Todesco S, Van Eck J, Buels RM, Bombarely A, Gosselin JR, Huang M, Leto JA, Menda N, Strickler S, Mao L, Gao S, Tecle IY, York T, Zheng Y, Vrebalov JT, Lee J, Zhong S, Mueller LA, Stiekema WJ, Ribeca P, Alioto T, Yang W, Huang S, Du Y, Zhang Z, Gao J, Guo Y, Wang X, Li Y, He J, Li C, Cheng Z, Zuo J, Ren J, Zhao J, Yan L, Jiang H, Wang B, Li H, Li Z, Fu F, Chen B, Feng Q, Fan D, Wang Y, Ling H, Xue Y, Ware D, McCombie WR, Lippman ZB, Chia JM, Jiang K, Pasternak S, Gelley L, Kramer M, Anderson LK, Chang SB, Royer SM, Shearer LA, Stack SM, Rose JK, Xu Y, Eannetta N, Matas AJ, McQuinn R, Tanksley SD, Camara F, Guigó R, Rombauts S, Fawcett J, Van de Peer Y, Zamir D, Liang C, Spannagl M, Gundlach H, Bruggmann R, Mayer K, Jia Z, Zhang J, Ye Z, Bishop GJ, Butcher S, Lopez-Cobollo R, Buchan D, Filippis I, Abbott J, Dixit R, Singh M, Singh A, Pal JK, Pandit A, Singh PK, Mahato AK, Gaikwad VD, Sharma RR, Mohapatra T, Singh NK, Causse M, Rothan C, Schiex T, Noirot C, Bellec A, Klopp C, Delalande C, Berges H, Mariette J, Frasse P, Vautrin S, Zouine M, Latché A, Rousseau C, Regad F, Pech JC, Philippot M, Bouzayen M, Pericard P, Osorio S, Fernandez del Carmen A, Monforte A, Granell A, Fernandez-Muñoz R, Conte M, Lichtenstein G, Carrari F, De Bellis G, Fuligni F, Peano C, Grandillo S, Termolino P, Pietrella M, Fantini E, Falcone G, Fiore A, Giuliano G, Lopez L, Facella P, Perotta G, Daddiego L, Bryan G, Orozco M, Pastor X, Torrents D, van Schriek MG, Feron RM, van Oeveren J, de Heer P, daponte L, Jacobs-Oomen S, Cariaso M, Prins M, van Eijk MJ, Janssen A, van Haaren MJ, Jungeun Kim SH, Kwon SY, Kim S, Koo DH, Lee S, Hur CG, Clouser C, Rico A, Hallab A, Gebhardt C, Klee K, Jöcker A, Warfsmann J, Göbel U, Kawamura S, Yano K, Sherman JD, Fukuoka H, Negoro S, Bhutty S, Chowdhury P, Chattopadhyay D, Datema E, Smit S, Schijlen EG, van de Belt J, van Haarst JC, Peters SA, van Staveren MA, Henkens MH, Mooyman PJ, Hesselink T, van Ham RC, Jiang G, Droege M, Choi D, Kang BC, Kim BD, Park M, Kim S, Yeom SI, Lee YH, Choi YD, Li G, Gao J, Liu Y, Huang S, Fernandez-Pedrosa V, Collado C, Zuñiga S, Wang G, Cade R, Dietrich RA, Rogers J, Knapp S, Fei Z, White RA, Thannhauser TW, Giovannoni JJ, Botella MA, Gilbert L, Gonzalez R, Goicoechea JL, Yu Y, Kudrna D, Collura K, Wissotski M, Wing R, Meyers BC, Gurazada AB, Green PJ, Vyas SM, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi AK, Dalmay T, Mohorianu I, Walts B, Chamala S, Barbazuk WB, Li J, Guo H, Lee TH, Wang Y, Zhang D, Paterson AH, Wang X, Tang H, Barone A, Chiusano ML, Ercolano MR, D'Agostino N, Di Filippo M, Traini A, Sanseverino W, Frusciante L, Seymour GB, Elharam M, Fu Y, Hua A, Kenton S, Lewis J, Lin S, Najar F, Lai H, Qin B, Qu C, Shi R, White D, White J, Xing Y, Yang K, Yi J, Yao Z, Zhou L, Roe BA, Vezzi A, D'Angelo M, Zimbello R, Schiavon R, Caniato E, Rigobello C, Campagna D, Vitulo N, Valle G, Nelson DR, De Paoli E, Szinay D, de Jong HH, Bai Y, Visser RG, Klein R, Beasley H, McLaren K, Nicholson C, Riddle C, Gianese G. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. NATURE May 30;485(7400): doi: /nature Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ. (2011). Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage. PLANT CELL Dec;23(12): doi: /tpc Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, Gonzales AJ, Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier JD, Meyers BC (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting sirnas. GENES DEV Dec 1;25(23): doi: /gad Morgante M, De Paoli E (2011). Toward the conifer genome sequence. In Genetics, Genomics and Breeding of Conifers Trees. Edited by Plomion C, Bousquet J, Kole C. New York: Edenbridge Science Publishers and CRC Press; 2011:: Wei F. S, Stein J. C, Liang C. Z, Zhang J. W, Fulton R. S, Baucom R. S, De Paoli E, Zhou S. G, Yang L. X, Han Y. J, Pasternak S, Narechania A, Zhang L. F, Yeh C. T, Ying K, Nagel D. H, Collura K, Kudrna D, Currie J, Lin J. K, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves T. A, Rock S. M, Adams S, Fulton L. A, Fronick C, Courtney W, 4

5 Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon J. M, Miguel P. S, Jiang N, Wessler S. R, Green P. J, Yu Y, Schwartz D. C, Meyers B. C, Bennetzen J. L, Martienssen R. A, Mccombie W. R, Aluru S, Clifton S. W, Schnable P. S, Ware D, Wilson R. K, Wing R. A (2010). Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet Nov;5(11):e doi: /journal.pgen Swaminathan K, Alabady M. S, Varala K, De Paoli E, Ho I, Rokhsar D. S, Arumuganathan A. K, Ming R, Green P. J, Meyers B. C, Moose S. P, Hudson M. E (2010). Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasse. Genome Biol. 2010;11(2):R12. doi: /gb r12. De Paoli E, Dorantes-Acosta A, Zhai J. X, Accerbi M, Jeong D. H, Park S, Meyers B. C, Jorgensen R. A, Green, P. J (2009). Distinct extremely abundant sirnas associated with cosuppression in petunia. RNA Nov;15(11): doi: /rna Vischi M, Fiori M, De Paoli E, Padovan S, Guarda M, Olivieri A (2008). Broccoli Fiolaro (Brassica oleracea), an endangered typical Italian cultivar. A genetic analysis by SSR markers. PLANT GENETIC RESOURCES, vol. 6(03), p , ISSN: Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vazquez M, Sidorenko L, Jeong D.H, Yen Y, Green P.J, Chandler V.L, Meyers B.C (2008). Distinct size distribution of endogenous sirnas in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A Sep 30;105(39): doi: /pnas German M.A, Pillay M, Jeong D.H, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis L.A, Nobuta K, German R, De Paoli E, Lu, C. Schroth G, Meyers B.C, Green P.J (2008). Global identification of microrna-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol Aug;26(8): doi: /nbt1417. Morgante M, De Paoli E, Radovic S (2007). Transposable elements and the plant pan-genomes. Curr Opin Plant Biol Apr;10(2): Vischi M, Arzenton F, De Paoli E, Paselli S, Tomat E, Olivieri A. M (2006). Identification of wild species of sunflower by a specific plastid DNA sequence. HELIA, vol. 29, p , ISSN: Heuertz M*, De Paoli E*, Kallman T*, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006). Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics Dec;174(4): *equally contributed De Paoli E*, Moroldo M*, Morgante M (2004). Marcatori molecolari e miglioramento genetico (Molecular markers and breeding). AGROINDUSTRIA, vol. 3,2, p , ISSN: *equally contributed ORAL PRESENTATIONS De Paoli E. and Morgante M. Nucleotide diversity and linkage disequilibrium in a set of candidate genes for time of bud set in Picea abies. Forest tree workshop; XIII Plant and animal genomes conference, San Diego (USA), De Paoli E. and Morgante M. Sequencing of large genomic regions in Norway spruce (Picea abies): an insight into a complex conifer genome. VIII FISV conference, Riva del Garda (Italy),

6 De Paoli E. and Morgante M. Sequencing of large genomic regions in Norway spruce (Picea abies): an insight into a complex conifer genome. Forest tree workshop; XV Plant and animal genomes conference, San Diego (USA), De Paoli E. et al. Comparative sequencing of small RNAs in plants. Small RNA workshop; XVII Plant and animal genomes conference, San Diego (USA), De Paoli E. et al. A comparative sequencing approach for the analysis of small RNAs in Grasses. Intl. Grass Genome Initiative (IGGI) workshop; XVII Plant and animal genomes conference, San Diego (USA), De Paoli E. et al. Single-base resolution of the grapevine methylome reveals the epigenomic landscape of a perennial fruit crop. 57 annual congress societa italiana di genetica agraria, Foggia (Italy), De Paoli E. et al. Single-base resolution of the grapevine methylome reveals the epigenomic landscape of a perennial fruit crop. EPIGEN annual meeting, Rome (Italy), LECTURES BY INVITATION The analysis of small RNAs and other applications of high-throughput sequencing technologies in Citrus. 7th Citrus Genomic Workshop. Oct 8-9 th 2008, Ft Pierce, Florida. High-throughput sequencing of small RNAs in plants. Fondazione Edmund Mach and Istituto agrario di San Michele all Adige. Jun 16 th 2009, S.Michele all Adige (TN), Italy. A small perspective of a great trip: the pervasive role of small RNAs in biology and evolution revealed by NGS data analysis.iga Workshop Next Generation Sequencing: from samples to data analysis. Istituto di Genomica Applicata (IGA). June 19 th -22 nd 2012 Udine, Italy. A glimpse on the grapevine epigenome emerging from whole genome and reduced representation BS-seq. EPIGEN Methylome Analysis Workshop, Jun th 2013, Padova, Italy. Challenged from inside and outside: plant epigenetic responses to genomic modifications and environmental cues. FISV 2014 XIII congress, Sep th 2014, Pisa, Italy. GRANTED PROJECTS "The control of plant root growth: a systems biology approach" (PRIN Italian funding program; coordinator Prof. Paolo Costantino, La Sapienza University, Rome). My role: responsible of research unit (small RNA and epigenomic analysis) PARTECIPATION TO EXISTING PROJECTS Novabreed (ERC; coordinator Prof. Michele Morgante, University of Udine). My role: team member, responsible for epigenomic analysis. Epigen (Italian Flagship Project; coordinator, Prof. Giuseppe Macino, La Sapienza University, Rome; responsible of research unit Prof. Michele Morgante). My role: collaborator, organization of sequencing services, small RNA and epigenomic analysis. 6

7 "The Epigenomic Plasticity of Grapevine in Genotype by Environment (GxE) Interactions" (FIRB, coordinator Dr. Silvia Dal Santo, University of Verona; responsible of research unit Dr. Cristian Del Fabbro). My role: team member. MEMBERSHIPS Member of the Italian Society of Agricultural Genetics (SIGA) REFERENCES Prof. Pamela J. Green, Ph.D., University of Delaware (UD) and Delaware Biotechnology Institute (DBI) Prof. Blake C. Meyers, Ph.D., University of Delaware (UD) and Delaware Biotechnology Institute (DBI) Prof. Michele Morgante, PhD., University of Udine (UNIUD) and Istituto di Genomica Applicata (IGA) Prof. Vincent Colot, PhD., Istitut de Biologie de l'école normale supérieure (IBENS) Dr. Azeddine Si-Ammour, PhD, Fondazione Edmund Mach (FEM) 7

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