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Grasso G, Rotunno S, Debruyne R, Bittner L, Miozzi L, Marmeisse R, Bianciotto V. Identification of DNA Viruses in Ancient DNA from Herbarium Samples. Methods Mol Biol 2024; 2732:221-234. [PMID: 38060128 DOI: 10.1007/978-1-0716-3515-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Herbaria encompass millions of plant specimens, mostly collected in the nineteenth and twentieth centuries that can represent a key resource for investigating the history and evolution of phytopathogens. In the last years, the application of high-throughput sequencing technologies for the analysis of ancient nucleic acids has revolutionized the study of ancient pathogens including viruses, allowing the reconstruction of historical genomic viral sequences, improving phylogenetic based molecular dating, and providing essential insight into plant virus ecology. In this chapter, we describe a protocol to reconstruct ancient plant and soil viral sequences starting from highly fragmented ancient DNA extracted from herbarium plants and their associated rhizospheric soil. Following Illumina high-throughput sequencing, sequence data are de novo assembled, and DNA viral sequences are selected, according to their similarity with known viruses.
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Affiliation(s)
- Gianluca Grasso
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi of Turin, Turin, Italy
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Silvia Rotunno
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Régis Debruyne
- Muséum National d'Histoire Naturelle, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE: UMR 7209 CNRS-MNHN), Paris, France
| | - Lucie Bittner
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France
- Institut Universitaire de France, Paris, France
| | - Laura Miozzi
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy
| | - Roland Marmeisse
- Muséum National d'Histoire Naturelle, Institut Systématique Evolution, Biodiversité, (ISYEB: UMR7205 CNRS-MNHN-Sorbonne Université-EPHE-UA), Paris, France.
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy.
| | - Valeria Bianciotto
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Turin, Italy.
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Cocozza C, Bartolini P, Brunetti C, Miozzi L, Pignattelli S, Podda A, Scippa GS, Trupiano D, Rotunno S, Brilli F, Maserti BE. Modulation of class III peroxidase pathways and phenylpropanoids in Arundo donax under salt and phosphorus stress. Plant Physiol Biochem 2022; 183:151-159. [PMID: 35598532 DOI: 10.1016/j.plaphy.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/01/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Arundo donax L. is an invasive species that has been recently employed for biomass production due to its well-known ability to colonize harsh environment. Based on previous observations, the present study investigated the potential role of phenylpropanoids and class III peroxidases to confer adaptation through biochemical and transcriptomic analysis in A. donax after Na+ and P excess supply, both in single stress and in combination, and after growth at low P level. The levels of hydrogen peroxide, flavonoids (i.e., quercetin, apigenin and kaempferol derivatives) and the activity of class III peroxidases, as well as the expression of several genes encoding for their enzymes involved in their biosynthesis, increased when Na+ was supplied in combination with P. These results suggest that those biomolecules are involved in the response of A. donax, to the presence of +Na and P in the soil. Moreover, even though at the sampling time no significant accumulation of lignin has been determined, the trend of accumulation of such metabolite and most of all the increase of several transcripts involved in its synthesis was found. This work for the first time indicates the need for further investigation devoted to elucidating whether the strengthening of cell walls via lignin synthesis is one of the mechanisms used by A. donax to adapt to harsh environments.
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Affiliation(s)
- C Cocozza
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50145, Florence, Italy.
| | - P Bartolini
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
| | - C Brunetti
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
| | - L Miozzi
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
| | - S Pignattelli
- CNR-IBBR - Institute of Biosciences and Bioresourses, via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - A Podda
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
| | - G S Scippa
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
| | - D Trupiano
- Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
| | - S Rotunno
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy; Department of Biosciences and Territory, University of Molise, 86090, Pesche, Italy
| | - F Brilli
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
| | - B E Maserti
- CNR-IPSP- National Research Council, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135, Torino, Italy
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Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
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4
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Tabein S, Miozzi L, Matić S, Accotto GP, Noris E. No Evidence for Seed Transmission of Tomato Yellow Leaf Curl Sardinia Virus in Tomato. Cells 2021; 10:cells10071673. [PMID: 34359841 PMCID: PMC8306144 DOI: 10.3390/cells10071673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 11/24/2022] Open
Abstract
Seed transmission is an important factor in the epidemiology of plant pathogens. Geminiviruses are serious pests spread in tropical and subtropical regions. They are transmitted by hemipteran insects, but a few cases of transmission through seeds were recently reported. Here, we investigated the tomato seed transmissibility of the begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), one of the agents inducing the tomato yellow leaf curl disease, heavily affecting tomato crops in the Mediterranean area. None of the 180 seedlings originating from TYLCSV-infected plants showed any phenotypic alteration typical of virus infection. Moreover, whole viral genomic molecules could not be detected in their cotyledons and true leaves, neither by membrane hybridization nor by rolling-circle amplification followed by PCR, indicating that TYLCSV is not a seed-transmissible pathogen for tomato. Examining the localization of TYLCSV DNA in progenitor plants, we detected the virus genome by PCR in all vegetative and reproductive tissues, but viral genomic and replicative forms were found only in leaves, flowers and fruit flesh, not in seeds and embryos. Closer investigations allowed us to discover for the first time that these embryos were superficially contaminated by TYLCSV DNA but whole genomic molecules were not detectable. Therefore, the inability of TYLCSV genomic molecules to colonize tomato embryos during infection justifies the lack of seed transmissibility observed in this host.
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Affiliation(s)
- Saeid Tabein
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, 10135 Torino, Italy; (S.T.); (S.M.); (G.P.A.)
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz 61349, Iran
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, 10135 Torino, Italy; (S.T.); (S.M.); (G.P.A.)
- Correspondence: (L.M.); (E.N.); Tel.: +39-011-3977-942 (L.M.); +39-011-3977-916 (E.N.)
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, 10135 Torino, Italy; (S.T.); (S.M.); (G.P.A.)
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, 10135 Torino, Italy; (S.T.); (S.M.); (G.P.A.)
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, 10135 Torino, Italy; (S.T.); (S.M.); (G.P.A.)
- Correspondence: (L.M.); (E.N.); Tel.: +39-011-3977-942 (L.M.); +39-011-3977-916 (E.N.)
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5
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Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reynard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021; 9:841. [PMID: 33920047 PMCID: PMC8071028 DOI: 10.3390/microorganisms9040841] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lucie Tamisier
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Ian Adams
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Neil Boonham
- Institute for Agri-Food Research and Innovation, Newcastle University, King’s Rd, Newcastle Upon Tyne NE1 7RU, UK;
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council, Via Amendola, 122/D, 70126 Bari, Italy;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
| | - Jan F. Kreuze
- International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima 15023, Peru;
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK;
| | - Martha Malapi-Wight
- Biotechnology Risk Analysis Programs, Biotechnology Regulatory Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD 20737, USA;
| | - Paolo Margaria
- Leibniz Institute-DSMZ, Inhoffenstrasse 7b, 38124 Braunschweig, Germany;
| | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia;
| | - Sam McGreig
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Benoit Remenant
- ANSES Plant Health Laboratory, 7 Rue Jean Dixméras, CEDEX 01, 49044 Angers, France;
| | | | - Johan Rollin
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
- DNAVision, 6041 Charleroi, Belgium
| | - Mike Rott
- Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada;
| | - Olivier Schumpp
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (J.-S.R.); (O.S.)
| | - Sébastien Massart
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
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6
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Tabein S, Jansen M, Noris E, Vaira AM, Marian D, Behjatnia SAA, Accotto GP, Miozzi L. The Induction of an Effective dsRNA-Mediated Resistance Against Tomato Spotted Wilt Virus by Exogenous Application of Double-Stranded RNA Largely Depends on the Selection of the Viral RNA Target Region. Front Plant Sci 2020; 11:533338. [PMID: 33329620 PMCID: PMC7732615 DOI: 10.3389/fpls.2020.533338] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 11/09/2020] [Indexed: 06/02/2023]
Abstract
Tomato spotted wilt virus (TSWV) is a devastating plant pathogen, causing huge crop losses worldwide. Unfortunately, due to its wide host range and emergence of resistance breaking strains, its management is challenging. Up to now, resistance to TSWV infection based on RNA interference (RNAi) has been achieved only in transgenic plants expressing parts of the viral genome or artificial microRNAs targeting it. Exogenous application of double-stranded RNAs (dsRNAs) for inducing virus resistance in plants, namely RNAi-based vaccination, represents an attractive and promising alternative, already shown to be effective against different positive-sense RNA viruses and viroids. In the present study, the protection efficacy of exogenous application of dsRNAs targeting the nucleocapsid (N) or the movement protein (NSm) coding genes of the negative-sense RNA virus TSWV was evaluated in Nicotiana benthamiana as model plant and in tomato as economically important crop. Most of the plants treated with N-targeting dsRNAs, but not with NSm-targeting dsRNAs, remained asymptomatic until 40 (N. benthamiana) and 63 (tomato) dpi, while the remaining ones showed a significant delay in systemic symptoms appearance. The different efficacy of N- and NSm-targeting dsRNAs in protecting plants is discussed in the light of their processing, mobility and biological role. These results indicate that the RNAi-based vaccination is effective also against negative-sense RNA viruses but emphasize that the choice of the target viral sequence in designing RNAi-based vaccines is crucial for its success.
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Affiliation(s)
- Saeid Tabein
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Marco Jansen
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Daniele Marian
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | | | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Turin, Italy
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7
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Miozzi L, Vaira AM, Brilli F, Casarin V, Berti M, Ferrandino A, Nerva L, Accotto GP, Lanfranco L. Arbuscular Mycorrhizal Symbiosis Primes Tolerance to Cucumber Mosaic Virus in Tomato. Viruses 2020; 12:E675. [PMID: 32580438 PMCID: PMC7354615 DOI: 10.3390/v12060675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 01/30/2023] Open
Abstract
Tomato plants can establish symbiotic interactions with arbuscular mycorrhizal fungi (AMF) able to promote plant nutrition and prime systemic plant defenses against pathogens attack; the mechanism involved is known as mycorrhiza-induced resistance (MIR). However, studies on the effect of AMF on viral infection, still limited and not conclusive, indicate that AMF colonization may have a detrimental effect on plant defenses against viruses, so that the term "mycorrhiza-induced susceptibility" (MIS) has been proposed for these cases. To expand the case studies to a not yet tested viral family, that is, Bromoviridae, we investigated the effect of the colonization by the AMF Funneliformis mosseae on cucumber mosaic virus (CMV) infection in tomato by phenotypic, physiological, biochemical, and transcriptional analyses. Our results showed that the establishment of a functional AM symbiosis is able to limit symptoms development. Physiological and transcriptomic data highlighted that AMF mitigates the drastic downregulation of photosynthesis-related genes and the reduction of photosynthetic CO2 assimilation rate caused by CMV infection. In parallel, an increase of salicylic acid level and a modulation of reactive oxygen species (ROS)-related genes, toward a limitation of ROS accumulation, was specifically observed in CMV-infected mycorrhizal plants. Overall, our data indicate that the AM symbiosis influences the development of CMV infection in tomato plants and exerts a priming effect able to enhance tolerance to viral infection.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Federico Brilli
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Unit of Sesto Fiorentino (FI), Via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy;
| | - Valerio Casarin
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Mara Berti
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Alessandra Ferrandino
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy;
| | - Luca Nerva
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
- Council for Agricultural Research and Economics—Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Strada delle Cacce 73, 10135 Torino, Italy; (A.M.V.); (V.C.); (M.B.); (L.N.); (G.P.A.)
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
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8
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Silvestri A, Turina M, Fiorilli V, Miozzi L, Venice F, Bonfante P, Lanfranco L. Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita. Front Microbiol 2020; 11:395. [PMID: 32231650 PMCID: PMC7082362 DOI: 10.3389/fmicb.2020.00395] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/26/2020] [Indexed: 01/01/2023] Open
Abstract
RNA interference (RNAi) is a key regulatory pathway of gene expression in almost all eukaryotes. This mechanism relies on short non-coding RNA molecules (sRNAs) to recognize in a sequence-specific manner DNA or RNA targets leading to transcriptional or post-transcriptional gene silencing. To date, the fundamental role of sRNAs in the regulation of development, stress responses, defense against viruses and mobile elements, and cross-kingdom interactions has been extensively studied in a number of biological systems. However, the knowledge of the “RNAi world” in arbuscular mycorrhizal fungi (AMF) is still limited. AMF are obligate mutualistic endosymbionts of plants, able to provide several benefits to their partners, from improved mineral nutrition to stress tolerance. Here we described the RNAi-related genes of the AMF Gigaspora margarita and characterized, through sRNA sequencing, its complex small RNAome, considering the possible genetic sources and targets of the sRNAs. G. margarita indeed is a mosaic of different genomes since it hosts endobacteria, RNA viruses, and non-integrated DNA fragments corresponding to mitovirus sequences. Our findings show that G. margarita is equipped with a complete set of RNAi-related genes characterized by the expansion of the Argonaute-like (AGO-like) gene family that seems a common trait of AMF. With regards to sRNAs, we detected populations of sRNA reads mapping to nuclear, mitochondrial, and viral genomes that share similar features (25-nt long and 5′-end uracil read enrichments), and that clearly differ from sRNAs of endobacterial origin. Furthermore, the annotation of nuclear loci producing sRNAs suggests the occurrence of different sRNA-generating processes. In silico analyses indicate that the most abundant G. margarita sRNAs, including those of viral origin, could target transcripts in the host plant, through a hypothetical cross-kingdom RNAi.
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Affiliation(s)
- Alessandro Silvestri
- Department of Life Sciences and Systems Biology, School of Nature Sciences, University of Turin, Turin, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, Italian National Research Council, Turin, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, School of Nature Sciences, University of Turin, Turin, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, Italian National Research Council, Turin, Italy
| | - Francesco Venice
- Department of Life Sciences and Systems Biology, School of Nature Sciences, University of Turin, Turin, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, School of Nature Sciences, University of Turin, Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, School of Nature Sciences, University of Turin, Turin, Italy
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9
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Cocozza C, Brilli F, Miozzi L, Pignattelli S, Rotunno S, Brunetti C, Giordano C, Pollastri S, Centritto M, Accotto GP, Tognetti R, Loreto F. Impact of high or low levels of phosphorus and high sodium in soils on productivity and stress tolerance of Arundo donax plants. Plant Sci 2019; 289:110260. [PMID: 31623790 DOI: 10.1016/j.plantsci.2019.110260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
The potential of Arundo donax to grow in degraded soils, characterized by excess of salinity (Na+), and phosphorus deficiency (-P) or excess (+P) also coupled with salinity (+NaP), was investigated by combining in vivo plant phenotyping, quantification of metabolites and ultrastructural imaging of leaves with a transcriptome-wide screening. Photosynthesis and growth were impaired by + Na, -P and + NaP. While + Na caused stomatal closure, enhanced biosynthesis of carotenoids, sucrose and isoprene and impaired anatomy of cell walls, +P negatively affected starch production and isoprene emission, and damaged chloroplasts. Finally, +NaP largely inhibited photosynthesis due to stomatal limitations, increased sugar content, induced/repressed a number of genes 10 time higher with respect to + P and + Na, and caused appearance of numerous and large plastoglobules and starch granules in chloroplasts. Our results show that A. donax is sensitive to unbalances of soil ion content, despite activation of defensive mechanisms that enhance plant resilience, growth and biomass production of A. donax under these conditions.
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Affiliation(s)
- Claudia Cocozza
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy; Department of Agriculture, Food, Environment and Forestry, Via San Bonaventura 13, 50145 Florence, Italy.
| | - Federico Brilli
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Laura Miozzi
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy
| | - Sara Pignattelli
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Silvia Rotunno
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy; Department of Biosciences and Territory, University of Molise, contrada Fonte Lappone, 86090 Pesche, Italy
| | - Cecilia Brunetti
- National Research Council of Italy, Institute for BioEconomy (IBE), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Cristiana Giordano
- National Research Council of Italy, Institute for BioEconomy (IBE), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Susanna Pollastri
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Mauro Centritto
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Gian Paolo Accotto
- National Research Council of Italy, Institute for the Sustainable Plant Protection (CNR - IPSP), Strada delle Cacce 73, 10135 Torino, Italy
| | - Roberto Tognetti
- Department of Agriculture, Environment and Food Sciences, University of Molise, Via Francesco De Sanctis, 86100 Campobasso, Italy; The EFI Project Centre on Mountain Forests (MOUNTFOR), Edmund Mach Foundation, 38010 San Michele all'Adige, Italy
| | - Francesco Loreto
- National Research Council of Italy, Department of Biology, Agriculture, and Food Sciences, Piazzale Aldo Moro 7, Roma, Italy; Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Napoli, Italy
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10
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Mandrile L, Rotunno S, Miozzi L, Vaira AM, Giovannozzi AM, Rossi AM, Noris E. Nondestructive Raman Spectroscopy as a Tool for Early Detection and Discrimination of the Infection of Tomato Plants by Two Economically Important Viruses. Anal Chem 2019; 91:9025-9031. [PMID: 31265250 DOI: 10.1021/acs.analchem.9b01323] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Global population forecasts dictate a rapid adoption of multifaceted approaches to fulfill increasing food requirements, ameliorate food dietary value and security using sustainable and economically feasible agricultural processes. Plant pathogens induce up to 25% losses in vegetable crops and their early detection would contribute to limit their spread and economic impact. As an alternative to time-consuming, destructive, and expensive diagnostic procedures, such as immunological assays and nucleic acid-based techniques, Raman spectroscopy (RS) is a nondestructive rapid technique that generates a chemical fingerprinting of a sample, at low operating costs. Here, we assessed the suitability of RS combined to chemometric analysis to monitor the infection of an important vegetable crop plant, tomato, by two dangerous and peculiarly different viral pathogens, Tomato yellow leaf curl Sardinia virus (TYLCSV) and Tomato spotted wilt virus (TSWV). Experimentally inoculated plants were monitored over 28 days for symptom occurrence and subjected to RS analysis, alongside with measuring the virus amount by quantitative real-time PCR. RS allowed to discriminate mock inoculated (healthy) from virus-infected specimens, reaching an accuracy of >70% after only 14 days after inoculation for TYLCSV and >85% only after 8 days for TSWV, demonstrating its suitability for early detection of virus infection. Importantly, RS also highlighted spectral differences induced by the two viruses, providing specific information on the infecting agent.
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Affiliation(s)
- Luisa Mandrile
- Istituto Nazionale di Ricerca Metrologica , Strada delle Cacce, 91 , 10135 , Torino , Italy
| | - Silvia Rotunno
- Institute for Sustainable Plant Protection, National Research Council of Italy , Strada delle Cacce, 73 , 10135 , Torino , Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy , Strada delle Cacce, 73 , 10135 , Torino , Italy
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy , Strada delle Cacce, 73 , 10135 , Torino , Italy
| | - Andrea M Giovannozzi
- Istituto Nazionale di Ricerca Metrologica , Strada delle Cacce, 91 , 10135 , Torino , Italy
| | - Andrea M Rossi
- Istituto Nazionale di Ricerca Metrologica , Strada delle Cacce, 91 , 10135 , Torino , Italy
| | - Emanuela Noris
- Institute for Sustainable Plant Protection, National Research Council of Italy , Strada delle Cacce, 73 , 10135 , Torino , Italy
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11
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Miozzi L, Vaira AM, Catoni M, Fiorilli V, Accotto GP, Lanfranco L. Arbuscular Mycorrhizal Symbiosis: Plant Friend or Foe in the Fight Against Viruses? Front Microbiol 2019; 10:1238. [PMID: 31231333 PMCID: PMC6558290 DOI: 10.3389/fmicb.2019.01238] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Plant roots establish interactions with several beneficial soil microorganisms including arbuscular mycorrhizal fungi (AMF). In addition to promoting plant nutrition and growth, AMF colonization can prime systemic plant defense and enhance tolerance to a wide range of environmental stresses and below-ground pathogens. A protective effect of the AMF against above-ground pathogens has also been described in different plant species, but it seems to largely rely on the type of attacker. Viruses are obligate biotrophic pathogens able to infect a large number of plant species, causing massive losses in crop yield worldwide. Despite their economic importance, information on the effect of the AM symbiosis on viral infection is limited and not conclusive. However, several experimental evidences, obtained under controlled conditions, show that AMF colonization may enhance viral infection, affecting susceptibility, symptomatology and viral replication, possibly related to the improved nutritional status and to the delayed induction of pathogenesis-related proteins in the mycorrhizal plants. In this review, we give an overview of the impact of the AMF colonization on plant infection by pathogenic viruses and summarize the current knowledge of the underlying mechanisms. For the cases where AMF colonization increases the susceptibility of plants to viruses, the term "mycorrhiza-induced susceptibility" (MIS) is proposed.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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12
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Silvestri A, Fiorilli V, Miozzi L, Accotto GP, Turina M, Lanfranco L. In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant. BMC Genomics 2019; 20:169. [PMID: 30832582 PMCID: PMC6399891 DOI: 10.1186/s12864-019-5561-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/22/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are short non-coding RNA molecules (20-30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from "donor" to "receiver" organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress. RESULTS Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization. CONCLUSIONS The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization.
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Affiliation(s)
- Alessandro Silvestri
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection – CNR Torino, Strada delle Cacce 73, 10131 Torino, Italy
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, 10125 Torino, Italy
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Chiumenti M, Catacchio CR, Miozzi L, Pirovano W, Ventura M, Pantaleo V. A Short Indel-Lacking-Resistance Gene Triggers Silencing of the Photosynthetic Machinery Components Through TYLCSV-Associated Endogenous siRNAs in Tomato. Front Plant Sci 2018; 9:1470. [PMID: 30364213 PMCID: PMC6193080 DOI: 10.3389/fpls.2018.01470] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/19/2018] [Indexed: 05/27/2023]
Abstract
Plant viruses modify gene expression in infected tissues by altering the micro (mi)RNA-mediated regulation of genes. Among conserved miRNA targets there are transcripts coding for transcription factors, RNA silencing core, and disease-resistance proteins. Paralogs in these gene families are widely present in plant genomes and are known to respond differently to miRNA-mediated regulation during plant virus infections. Using genome-wide approaches applied to Solanum lycopersicum infected by a nuclear-replicating virus, we highlighted miRNA-mediated cleavage events that could not be revealed in virus-free systems. Among them we confirmed miR6024 targeting and cleavage of RX-coiled-coil (RX-CC), nucleotide binding site (NBS), leucine-rich (LRR) mRNA. Cleavage of paralogs was associated with short indels close to the target sites, indicating a general functional significance of indels in fine-tuning gene expression in plant-virus interaction. miR6024-mediated cleavage, uniquely in virus-infected tissues, triggers the production of several 21-22 nt secondary siRNAs. These secondary siRNAs, rather than being involved in the cascade regulation of other NBS-LRR paralogs, explained cleavages of several mRNAs annotated as defence-related proteins and components of the photosynthetic machinery. Outputs of these data explain part of the phenotype plasticity in plants, including the appearance of yellowing symptoms in the viral pathosystem.
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Affiliation(s)
- Michela Chiumenti
- Institute for Sustainable Plant Protection of the National Research Council, Research Unit of Bari, Bari, Italy
| | | | - Laura Miozzi
- Institute for Sustainable Plant Protection of the National Research Council, Research Unit of Turin, Turin, Italy
| | | | - Mario Ventura
- Dipartimento di Biologia, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection of the National Research Council, Research Unit of Bari, Bari, Italy
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14
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Vaira AM, Lim HS, Bauchan G, Gulbronson CJ, Miozzi L, Vinals N, Natilla A, Hammond J. The interaction of Lolium latent virus major coat protein with ankyrin repeat protein NbANKr redirects it to chloroplasts and modulates virus infection. J Gen Virol 2018; 99:730-742. [PMID: 29557771 DOI: 10.1099/jgv.0.001043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lolium latent virus (LoLV) major coat protein sequence contains a typical chloroplast transit peptide (cTP) domain. In infected Nicotiana benthamiana leaf tissue, LoLV coat proteins can be detected at the chloroplast. In transient expression, several N-terminal deletions of the CP sequence, increasing in length, result in disruption of the domain functionality, markedly affecting intracellular localization. A yeast two-hybrid-based study using LoLV CP as bait identified several potentially interacting Arabidopsis host proteins, most of them with chloroplast-linked pathways. One of them, an ankyrin repeat protein, was studied in detail. The N. benthamiana homologue (NbANKr) targets chloroplasts, is able to co-localize with LoLV CP at chloroplast membranes in transient expression and shows a robust interaction with LoLV CP in vivo by BiFC, which has been confirmed by yeast two-hybrid data. Silencing NbANKr genes in N. benthamiana plants, prior to challenging with LoLV by mechanical inoculation, affects LoLV infection, significantly reducing the level of viral RNA in young leaves, compared to levels in control plants, and suggesting an inhibition of virus movement. Silencing of NbANKr has no obvious effect on plant phenotype, but is able to interfere with LoLV infection, opening the way for a new strategy for virus infection control.
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Affiliation(s)
- A M Vaira
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
| | - H S Lim
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
- Department of Applied Biology, Chungnam National University, Daejeon, 305-764, Republic of Korea
| | - G Bauchan
- USDA-ARS, BARC, Electron and Confocal Microscopy Unit, 10300 Baltimore Ave, Beltsville, MD, USA
| | - C J Gulbronson
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education (ORISE) Postdoctoral Fellow, USA
| | - L Miozzi
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - N Vinals
- Institute for Sustainable Plant Protection, IPSP-CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - A Natilla
- USDA-ARS, BARC, Molecular Plant Pathology Laboratory, 10300 Baltimore Ave, Beltsville, MD, USA
- Present address: Arc Horizon, LLC, Innovation Park, 1736 West Paul Dirac Dr., Tallahassee, FL, USA
| | - J Hammond
- USDA-ARS, USNA, Floral and Nursery Plant Research Unit, 10300 Baltimore Ave, Beltsville, MD, USA
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15
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Zaagueri T, Miozzi L, Mnari-Hattab M, Noris E, Accotto GP, Vaira AM. Deep Sequencing Data and Infectivity Assays Indicate that Chickpea Chlorotic Dwarf Virus is the Etiological Agent of the "Hard Fruit Syndrome" of Watermelon. Viruses 2017; 9:E311. [PMID: 29068372 PMCID: PMC5707518 DOI: 10.3390/v9110311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 11/25/2022] Open
Abstract
Chickpea chlorotic dwarf virus (CpCDV), a polyphagous mastrevirus, family Geminiviridae, has been recently linked to the onset of the "hard fruit syndrome" of watermelon, first described in Tunisia, that makes fruits unmarketable due to the presence of white hard portions in the flesh, chlorotic mottling on the rind, and an unpleasant taste. To investigate the etiological agent of this disease, total RNA extracted from symptomatic watermelon fruits was subjected to small RNA sequencing through next generation sequencing (NGS) techniques. Data obtained showed the presence of CpCDV and two other viral species. However, following validation through polymerase chain reaction (PCR), CpCDV was the only viral species consistently detected in all samples. Watermelon seedlings were then challenged by an agroinfectious CpCDV clone; several plants proved to be CpCDV-infected, and were able to produce fruits. CpCDV infected and replicated in watermelon fruits and leaves, leading to abnormality in fruits and in seed production, similar to those described in field. These results indicate that CpCDV is the etiological agent of the "hard fruit syndrome" of watermelon.
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Affiliation(s)
- Takoua Zaagueri
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Laura Miozzi
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Monia Mnari-Hattab
- Laboratoire de Biotechnologie Appliquée à l'Agriculture, Institut National de la Recherche Agronomique de Tunisie (INRAT), Université de Carthage, El Rue Hedi Karray Menzah, 1004 Tunis, Tunisia.
| | - Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection (IPSP), CNR, 10135 Turin, Italy.
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16
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Pantaleo V, Vitali M, Boccacci P, Miozzi L, Cuozzo D, Chitarra W, Mannini F, Lovisolo C, Gambino G. Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress. Sci Rep 2016; 6:20167. [PMID: 26833264 PMCID: PMC4735847 DOI: 10.1038/srep20167] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/22/2015] [Indexed: 02/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the post-transcriptional control of several pathway intermediates, thus playing pivotal roles in plant growth, development and response to biotic and abiotic stresses. In recent years, the grapevine genome release, small(s)-RNAseq and degradome-RNAseq together has allowed the discovery and characterisation of many miRNA species, thus rendering the discovery of additional miRNAs difficult and uncertain. Taking advantage of the miRNA responsiveness to stresses and the availability of virus-free Vitis vinifera plants and those infected only by a latent virus, we have analysed grapevines subjected to drought in greenhouse conditions. The sRNA-seq and other sequence-specific molecular analyses have allowed us to characterise conserved miRNA expression profiles in association with specific eco-physiological parameters. In addition, we here report 12 novel grapevine-specific miRNA candidates and describe their expression profile. We show that latent viral infection can influence the miRNA profiles of V. vinifera in response to drought. Moreover, study of eco-physiological parameters showed that photosynthetic rate, stomatal conductance and hydraulic resistance to water transport were significantly influenced by drought and viral infection. Although no unequivocal cause–effect explanation could be attributed to each miRNA target, their contribution to the drought response is discussed.
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Affiliation(s)
- Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Research Unit of Bari. Via Amendola 165/a, 70126 Bari, Italy
| | - Marco Vitali
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino. Strada delle Cacce 73, 10135 Torino, Italy
| | - Danila Cuozzo
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Franco Mannini
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Claudio Lovisolo
- Department of Agricultural, Forest and Food Sciences, University of Torino. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy.,Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Grugliasco Unit. Largo P. Braccini 2, 10095 Grugliasco-TO, Italy
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17
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Margaria P, Miozzi L, Ciuffo M, Rosa C, Axtell MJ, Pappu HR, Turina M. Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection. Virus Res 2016; 211:38-45. [PMID: 26432447 DOI: 10.1016/j.virusres.2015.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/22/2015] [Accepted: 09/25/2015] [Indexed: 11/19/2022]
Abstract
Viral small RNAs (vsRNAs) are one of the key elements involved in RNA silencing-based defense against viruses in plants. We analyzed the vsRNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot virus (PolRSV) (Tospovirus, Bunyaviridae). VsRNAs were abundant in both hosts, but a different size profile was observed, with an abundance peak at 21 in N. benthamiana and at 22 nt in tomato. VsRNAs mapping to the PolRSV L genomic segment were under-represented in both hosts, while S and M segments were differentially and highly targeted in N. benthamiana and tomato, respectively. Differences in preferential targeting of single ORFs were observed, with over-representation of NSs ORF-derived reads in N. benthamiana. Intergenic regions (IGRs)-mapping vsRNAs were under-represented, while enrichment of vsRNAs reads mapping to the NSs positive sense strand was observed in both hosts. Comparison with a previous study on tomato spotted wilt virus (TSWV) under the same experimental conditions, showed that the relative accumulation of PolRSV-specific and endogenous sRNAs was similar to the one observed for silencing suppressor-deficient TSWV strains, suggesting possible different properties of PolRSV NSs silencing suppressor compared to that of TSWV.
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Affiliation(s)
- Paolo Margaria
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Miozzi
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Marina Ciuffo
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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18
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Margaria P, Miozzi L, Rosa C, Axtell MJ, Pappu HR, Turina M. Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana. Virus Res 2015; 208:30-8. [PMID: 26047586 DOI: 10.1016/j.virusres.2015.05.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 01/01/2023]
Abstract
Tospoviruses are plant-infecting viruses belonging to the family Bunyaviridae. We used a collection of wild-type, phylogenetically distinct tomato spotted wilt virus isolates and related silencing-suppressor defective mutants to study the effects on the small RNA (sRNA) accumulation during infection of Nicotiana benthamiana. Our data showed that absence of a functional silencing suppressor determined a marked increase of the total amount of viral sRNAs (vsRNAs), and specifically of the 21 nt class. We observed a common under-representation of vsRNAs mapping to the intergenic region of S and M genomic segments, and preferential mapping of the reads against the viral sense open reading frames, with the exception of the NSs gene. The NSs-mutant strains showed enrichment of NSm-derived vsRNA compared to the expected amount based on gene size. Analysis of 5' terminal nucleotide preference evidenced a significant enrichment in U for the 21 nt- and in A for 24 nt-long endogenous sRNAs in all the samples. Hotspot analysis revealed a common abundant accumulation of reads at the 5' end of the L segment, mostly in the antiviral sense, for the NSs-defective isolates, suggesting that absence of the silencing suppressor can influence preferential targeting of the viral genome.
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Affiliation(s)
- Paolo Margaria
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Laura Miozzi
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, WA 99164, USA
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
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19
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Noris E, Miozzi L. Real-time PCR protocols for the quantification of the begomovirus tomato yellow leaf curl Sardinia virus in tomato plants and in its insect vector. Methods Mol Biol 2015; 1236:61-72. [PMID: 25287496 DOI: 10.1007/978-1-4939-1743-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV) (Geminiviridae) is an important pathogen, transmitted by the whitefly Bemisia tabaci, that severely affects the tomato production in the Mediterranean basin. Here, we describe real-time PCR protocols suitable for relative and absolute quantification of TYLCSV in tomato plants and in whitefly extracts. Using primers and probe specifically designed for TYLCSV, the protocols for relative quantification allow to compare the amount of TYLCSV present in different plant or whitefly samples, normalized to the amount of DNA present in each sample using endogenous tomato or Bemisia genes as internal references. The absolute quantification protocol allows to calculate the number of genomic units of TYLCSV over the genomic units of the plant host (tomato), with a sensitivity of as few as ten viral genome copies per sample. The described protocols are potentially suitable for several applications, such as plant breeding for resistance, analysis of virus replication, and virus-vector interaction studies.
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Affiliation(s)
- Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Strada delle Cacce 73, 10135, Torino, Italy,
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20
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Pirovano W, Miozzi L, Boetzer M, Pantaleo V. Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population. Front Microbiol 2015; 5:790. [PMID: 25674078 PMCID: PMC4307218 DOI: 10.3389/fmicb.2014.00790] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022] Open
Abstract
Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner. Currently a substantial number of studies have been performed which employ next generation sequencing techniques to either analyze known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Taking advantage of the well-known Cymbidium ringspot virus we have carried out a comparison of different bioinformatics tools to reconstruct the viral genome based on 21–27 nt short (s)RNA sequencing with the aim to identify the most efficient pipeline. The same approach was applied to a population of plants constituting an ancient variety of Cicer arietinum with red seeds. Among the discovered viruses, we describe the presence of a Tobamovirus referring to the Tomato mottle mosaic virus (NC_022230), which was not yet observed on C. arietinum nor revealed in Europe and a viroid referring to Hop stunt viroid (NC_001351.1) never reported in chickpea. Notably, a reference sequence guided approach appeared the most efficient in such kind of investigation. Instead, the de novo assembly reached a non-appreciable coverage although the most prominent viral species could still be identified. Advantages and limitations of viral metagenomics analysis using sRNAs are discussed.
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Affiliation(s)
- Walter Pirovano
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Laura Miozzi
- Institute for Sustainable Plant Protection of National Research Council Torino, Italy
| | - Marten Boetzer
- Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection of National Research Council, Bari Research Unit Bari, Italy
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21
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Abstract
Viruses are obligate intracellular entities that infect all forms of life. In plants, invading viral nucleic acids trigger RNA silencing machinery and it results in the accumulation of viral short interfering RNAs (v-siRNAs). The study of v-siRNAs population in biological samples has become a major part of many research projects aiming to identify viruses infecting them, including unknown viruses, even at extremely low titer. Currently, siRNA populations are investigated by high-throughput sequencing approaches, which generate very large data sets. The major difficulty in these studies is to properly analyze such huge amount of data. In this regard, easy-to-use bioinformatics tools to groom and decipher siRNA libraries and to draw out v-siRNAs are needed. Here we describe a workflow, which permit users with little experience in bioinformatics to draw out v-siRNAs from raw data sequences obtained by Illumina technology. Such pipeline has been released in the context of Galaxy, an open source Web-based platform for bioinformatics analyses.
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Affiliation(s)
- Laura Miozzi
- Institute for Sustainable Plant Protection of CNR, Strada delle Cacce 73, Turin, Italy
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Margaria P, Miozzi L, Ciuffo M, Pappu H, Turina M. The complete genome sequence of polygonum ringspot virus. Arch Virol 2014; 159:3149-52. [PMID: 25000901 DOI: 10.1007/s00705-014-2166-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
Abstract
The complete genome sequence of polygonum ringspot virus (PolRSV), genus Tospovirus, family Bunyaviridae, was determined. This is the first report of the complete genome sequence for a European tospovirus isolate. The large RNA of PolRSV was 8893 nucleotides (nt) in size and contained a single open reading frame of 8628 nucleotides in the viral-complementary sense, coding for a predicted RNA-dependent RNA polymerase of 330.9 kDa. Two untranslated regions of 230 and 32 nucleotides were present at the 5' and 3' termini, respectively, which showed conserved terminal sequences, as commonly observed for tospovirus genomic RNAs. The medium and small (S) RNAs were 4710 and 2485 nucleotides in size, respectively, and showed 99 % homology to the corresponding genomic segment of a previously partially characterized PolRSV isolate, Plg3. Protein sequences for GN/GC, N and NSs were identical in length in the two PolRSV isolates, while an amino acid insertion was observed for the NSm protein of the newly characterized isolate. The noncoding intergenic region of the S RNA was very short (183 nt) and was not predicted to form a hairpin structure, confirming that this unique characteristic within tospoviruses, previously observed for Plg3, is not isolate specific.
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Affiliation(s)
- P Margaria
- Istituto di Virologia Vegetale, Sez. di Torino, CNR, Strada delle Cacce 73, 10135, Turin, Italy
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Maffei G, Miozzi L, Fiorilli V, Novero M, Lanfranco L, Accotto GP. The arbuscular mycorrhizal symbiosis attenuates symptom severity and reduces virus concentration in tomato infected by Tomato yellow leaf curl Sardinia virus (TYLCSV). Mycorrhiza 2014; 24:179-86. [PMID: 24072193 DOI: 10.1007/s00572-013-0527-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/11/2013] [Indexed: 05/17/2023]
Abstract
The arbuscular mycorrhizal (AM) symbiosis is considered a natural instrument to improve plant health and productivity since mycorrhizal plants often show higher tolerance to abiotic and biotic stresses. However, the impact of the AM symbiosis on infection by viral pathogens is still largely uncertain and little explored. In the present study, tomato plants were grown under controlled conditions and inoculated with the AM fungus Funneliformis mosseae. Once the mycorrhizal colonization had developed, plants were inoculated with the Tomato yellow leaf curl Sardinia virus (TYLCSV), a geminivirus causing one of the most serious viral diseases of tomatoes in Mediterranean areas. Biological conditions consisted of control plants (C), TYLCSV-infected plants (V), mycorrhizal plants (M), and TYLCSV-infected mycorrhizal plants (MV). At the time of analysis, the level of mycorrhiza development and the expression profiles of mycorrhiza-responsive selected genes were not significantly modified by virus infection, thus indicating that the AM symbiosis was unaffected by the presence and spread of the virus. Viral symptoms were milder, and both shoot and root concentrations of viral DNA were lower in MV plants than in V plants. Overall F. mosseae colonization appears to exert a beneficial effect on tomato plants in attenuating the disease caused by TYLCSV.
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Affiliation(s)
- Giulia Maffei
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale Mattioli 25, 10125, Torino, Italy
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Zouari I, Salvioli A, Chialva M, Novero M, Miozzi L, Tenore GC, Bagnaresi P, Bonfante P. From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism. BMC Genomics 2014; 15:221. [PMID: 24655934 PMCID: PMC3997964 DOI: 10.1186/1471-2164-15-221] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 03/14/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression. To understand the systemic effect of the fungal symbiosis on the tomato fruit, we used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening stage. RESULTS Fruits were collected at 55 days after flowering, from plants colonized with Funneliformis mosseae and from control plants, which were fertilized to avoid responses related to nutrient deficiency. Transcriptome analysis identified 712 genes that are differentially expressed in fruits from mycorrhizal and control plants. Gene Ontology (GO) enrichment analysis of these genes showed 81 overrepresented functional GO classes. Up-regulated GO classes include photosynthesis, stress response, transport, amino acid synthesis and carbohydrate metabolism functions, suggesting a general impact of fungal symbiosis on primary metabolisms and, particularly, on mineral nutrition. Down-regulated GO classes include cell wall, metabolism and ethylene response pathways. Quantitative RT-PCR validated the RNA-Seq results for 12 genes out of 14 when tested at three fruit ripening stages, mature green, breaker and turning. Quantification of fruit nutraceutical and mineral contents produced values consistent with the expression changes observed by RNA-Seq analysis. CONCLUSIONS This RNA-Seq profiling produced a novel data set that explores the intersection of mycorrhization and fruit development. We found that the fruits of mycorrhizal plants show two transcriptomic "signatures": genes characteristic of a climacteric fleshy fruit, and genes characteristic of mycorrhizal status, like phosphate and sulphate transporters. Moreover, mycorrhizal plants under low nutrient conditions produce fruits with a nutrient content similar to those from non-mycorrhizal plants under high nutrient conditions, indicating that AM fungi can help replace exogenous fertilizer for fruit crops.
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Affiliation(s)
- Inès Zouari
- />Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Alessandra Salvioli
- />Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Matteo Chialva
- />Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Mara Novero
- />Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
| | - Laura Miozzi
- />Institute of Plant Virology-IVV-CNR, Strada Delle Cacce, 73, 10135 Turin, Italy
| | - Gian Carlo Tenore
- />Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Paolo Bagnaresi
- />Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S. Protaso, 302 I, 29017 Fiorenzuola d’Arda, PC, Italy
| | - Paola Bonfante
- />Department of Life Sciences and Systems Biology, University of Turin, Viale Mattioli 25, 10125 Turin, Italy
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Miozzi L, Napoli C, Sardo L, Accotto GP. Transcriptomics of the interaction between the monopartite phloem-limited geminivirus tomato yellow leaf curl Sardinia virus and Solanum lycopersicum highlights a role for plant hormones, autophagy and plant immune system fine tuning during infection. PLoS One 2014; 9:e89951. [PMID: 24587146 PMCID: PMC3938563 DOI: 10.1371/journal.pone.0089951] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/25/2014] [Indexed: 12/13/2022] Open
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV), a DNA virus belonging to the genus Begomovirus, causes severe losses in tomato crops. It infects only a limited number of cells in the vascular tissues, making difficult to detect changes in host gene expression linked to its presence. Here we present the first microarray study of transcriptional changes induced by the phloem-limited geminivirus TYLCSV infecting tomato, its natural host. The analysis was performed on the midrib of mature leaves, a material naturally enriched in vascular tissues. A total of 2206 genes were up-regulated and 1398 were down-regulated in infected plants, with an overrepresentation of genes involved in hormone metabolism and responses, nucleic acid metabolism, regulation of transcription, ubiquitin-proteasome pathway and autophagy among those up-regulated, and in primary and secondary metabolism, phosphorylation, transcription and methylation-dependent chromatin silencing among those down-regulated. Our analysis showed a series of responses, such as the induction of GA- and ABA-responsive genes, the activation of the autophagic process and the fine tuning of the plant immune system, observed only in TYLCSV-tomato compatible interaction so far. On the other hand, comparisons with transcriptional changes observed in other geminivirus-plant interactions highlighted common host responses consisting in the deregulation of biotic stress responsive genes, key enzymes in the ethylene biosynthesis and methylation cycle, components of the ubiquitin proteasome system and DNA polymerases II. The involvement of conserved miRNAs and of solanaceous- and tomato-specific miRNAs in geminivirus infection, investigated by integrating differential gene expression data with miRNA targeting data, is discussed.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Chiara Napoli
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Luca Sardo
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- Viral Recombination Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gian Paolo Accotto
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- * E-mail:
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Miozzi L, Pantaleo V, Burgyán J, Accotto GP, Noris E. Analysis of small RNAs derived from tomato yellow leaf curl Sardinia virus reveals a cross reaction between the major viral hotspot and the plant host genome. Virus Res 2013; 178:287-96. [PMID: 24091361 DOI: 10.1016/j.virusres.2013.09.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
RNA silencing is a defense mechanism exploited by plants against viruses. Upon infection, viral genomes and their transcripts are processed by Dicer-like (DCL) ribonucleases into viral small interfering RNAs (vsRNAs) of 21-24 nucleotides that further guide silencing of viral transcripts. To get an insight into the molecular interaction between tomato and the monopartite phloem-limited begomovirus tomato yellow leaf curl Sardinia virus (TYLCSV), a pathogen inducing a devastating disease of tomato in the Mediterranean region, we characterized by deep sequencing the vsRNA population in virus-infected tomato plants, using a Solexa/Illumina platform. TYLCSV-sRNAs spanned the entire viral genome but were discontinuously distributed throughout it, with a prevalence from the transcribed regions. TYLCSV-sRNAs were mainly 21-22 nucleotides in length and their polarity was asymmetrically distributed along the genome. The most abundant vsRNAs originated from a narrow region overlapping the Rep/C4 genes and from a broader region including the end of the V2 and the beginning of the coat protein genes. Deep sequencing results were validated by different hybridization techniques. Comparisons with the data available on vsRNAs for other begomoviruses highlighted both similarities and differences. Host-derived RNA species cross-reacting with a portion of the viral genome corresponding to the most abundant vsRNAs hotspot were detected. Bioinformatics analyses were carried out to investigate the nature of these host molecules.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 101035 Torino, Italy
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27
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Miozzi L, Gambino G, Burgyan J, Pantaleo V. Genome-wide identification of viral and host transcripts targeted by viral siRNAs in Vitis vinifera. Mol Plant Pathol 2013; 14:30-43. [PMID: 22947170 PMCID: PMC6638717 DOI: 10.1111/j.1364-3703.2012.00828.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, RNA silencing is a surveillance mechanism against invading viruses. It involves the production of virus-derived small interfering RNAs (vsiRNAs), which guide the RNA-induced silencing complex (RISC) to inactivate viruses. vsiRNAs may also promote the silencing of host mRNAs in a sequence-specific manner. In this work, vsiRNAs derived from two grapevine-infecting viruses (Grapevine fleck virus and Grapevine rupestris stem pitting-associated virus) were selected from cDNA libraries of short RNAs and were cross-referenced with the remnants of both cleaved host transcripts and viral RNAs from a degradome dataset. We identified dozens of host transcripts targeted by vsiRNAs. Among them, several encode putative proteins involved in ribosome biogenesis and in biotic and abiotic stresses. Moreover, we identified vsiRNAs which explain the cleavage sites in viral genomes. A consistent fraction of vsiRNAs did not apparently account for cleavage, suggesting that only a low percentage of vsiRNAs are involved in the antiviral response.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale del CNR, 10135, Torino, Italy
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28
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Davino S, Miozzi L, Panno S, Rubio L, Davino M, Accotto GP. Recombination profiles between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in laboratory and field conditions: evolutionary and taxonomic implications. J Gen Virol 2012; 93:2712-2717. [DOI: 10.1099/vir.0.045773-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tomato yellow leaf curl Sardinia virus and Tomato yellow leaf curl virus have co-existed in Italian tomato crops since 2002 and have reached equilibrium, with plants hosting molecules of both species plus their recombinants being the most frequent case. Recombination events are studied in field samples, as well as in experimental co-infections, when recombinants were detected as early as 45 days following inoculation. In both conditions, recombination breakpoints were essentially absent in regions corresponding to ORFs V2, CP and C4, whereas density was highest in the 3′-terminal portion of ORF C3, next to the region where the two transcription units co-terminate. The vast majority of breakpoints were mapped at antisense ORFs, supporting speculation that the rolling-circle replication mechanism, and the existence of sense and antisense ORFs on the circular genome, may result in clashes between replication and transcription complexes.
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Affiliation(s)
- Salvatore Davino
- DEMETRA Department, University of Palermo, Viale delle Scienze Ed. 5, 90100 Palermo, Italy
| | - Laura Miozzi
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
| | - Stefano Panno
- DEMETRA Department, University of Palermo, Viale delle Scienze Ed. 5, 90100 Palermo, Italy
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), crt Moncada-Náquera Km 4,5, 46113 Moncada (Valencia), Spain
| | - Mario Davino
- DISPA Department, University of Catania, Via S. Sofia 100, 95100 Catania, Italy
| | - Gian Paolo Accotto
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135, Torino, Italy
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29
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Miozzi L, Catoni M, Fiorilli V, Mullineaux PM, Accotto GP, Lanfranco L. Arbuscular mycorrhizal symbiosis limits foliar transcriptional responses to viral infection and favors long-term virus accumulation. Mol Plant Microbe Interact 2011; 24:1562-1572. [PMID: 21899386 DOI: 10.1094/mpmi-05-11-0116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Tomato (Solanum lycopersicum) can establish symbiotic interactions with arbuscular mycorrhizal (AM) fungi, and can be infected by several pathogenic viruses. Here, we investigated the impact of mycorrhization by the fungus Glomus mosseae on the Tomato spotted wilt virus (TSWV) infection of tomato plants by transcriptomic and hormones level analyses. In TSWV-infected mycorrhizal plants, the AM fungus root colonization limited virus-induced changes in gene expression in the aerial parts. The virus-responsive upregulated genes, no longer induced in infected mycorrhizal plants, were mainly involved in defense responses and hormone signaling, while the virus-responsive downregulated genes, no longer repressed in mycorrhizal plants, were involved in primary metabolism. The presence of the AM fungus limits, in a salicylic acid-independent manner, the accumulation of abscissic acid observed in response to viral infection. At the time of the molecular analysis, no differences in virus concentration or symptom severity were detected between mycorrhizal and nonmycorrhizal plants. However, in a longer period, increase in virus titer and delay in the appearance of recovery were observed in mycorrhizal plants, thus indicating that the plant's reaction to TSWV infection is attenuated by mycorrhization.
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30
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Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 2010; 408:49-56. [PMID: 20875658 DOI: 10.1016/j.virol.2010.09.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/16/2010] [Accepted: 09/01/2010] [Indexed: 01/20/2023]
Abstract
Virus-derived short interfering RNAs (vsiRNAs) isolated from grapevine V. vinifera Pinot Noir clone ENTAV 115 were analyzed by high-throughput sequencing using the Illumina Solexa platform. We identified and characterized vsiRNAs derived from grapevine field plants naturally infected with different viruses belonging to the genera Foveavirus, Maculavirus, Marafivirus and Nepovirus. These vsiRNAs were mainly of 21 and 22 nucleotides (nt) in size and were discontinuously distributed throughout Grapevine rupestris stem-pitting associated virus (GRSPaV) and Grapevine fleck virus (GFkV) genomic RNAs. Among the studied viruses, GRSPaV and GFkV vsiRNAs had a 5' terminal nucleotide bias, which differed from that described for experimental viral infections in Arabidopsis thaliana. VsiRNAs were found to originate from both genomic and antigenomic GRSPaV RNA strands, whereas with the grapevine tymoviruses GFkV and Grapevine Red Globe associated virus (GRGV), the large majority derived from the antigenomic viral strand, a feature never observed in other plant-virus interactions.
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Affiliation(s)
- Vitantonio Pantaleo
- Istituto di Virologia Vegetale del C.N.R., Strada delle Cacce 73, Turin, Italy.
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31
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Davino S, Miozzi L, Accotto GP. The complete nucleotide sequence of an isolate of Tomato yellow leaf curl Sardinia virus found in Sicily. Arch Virol 2010; 155:1539-42. [PMID: 20665057 DOI: 10.1007/s00705-010-0762-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
Abstract
Partial sequences of Tomato yellow leaf curl Sardinia virus (TYLCSV) derived from tomato samples collected in Sicily in 1999, 2002 and 2004 indicated the presence of a TYLCSV different from the one previously described as the Sic strain. Here, we report a complete DNA sequence that is classified as belonging to the TYLCSV type strain (Sar strain), confirming the co-existence in Sicily of virus populations of both strains. Moreover, comparisons between this new sequence and those of the two recombinants recently described in Sicily revealed unequivocally (99% identity) that their TYLCSV-derived portion originated from the Sar strain.
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Affiliation(s)
- Salvatore Davino
- Dipartimento di Scienze Entomologiche, Fitopatologiche, Microbiologiche e Zootecniche, Università degli Studi di Palermo, Viale delle Scienze, Palermo, Italy
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32
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Miozzi L, Provero P, Accotto GP. ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato. Plant Mol Biol 2010; 73:519-532. [PMID: 20411302 DOI: 10.1007/s11103-010-9638-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 04/11/2010] [Indexed: 05/29/2023]
Abstract
Co-expressed genes are often expected to be functionally related and many bioinformatics approaches based on co-expression have been developed to infer their biological role. However, such annotations may be unreliable, whereas the evolutionary conservation of gene co-expression among species may form a basis for more confident predictions. The huge amount of expression data (microarrays, SAGE, ESTs) has already allowed functional studies based on conserved co-expression in animals. Up to now, the implementation of analogous tools for plants has been strongly limited probably by the paucity and heterogeneity of data. Here we present ORTom, a tomato-centred EST data-mining approach based on conserved co-expression in the Solanaceae family. ORTom can be used to predict functional relationships among genes and to prioritize candidate genes for targeted studies. The method consists in ranking ESTs co-expressed with a gene of interest according to the level of expression pattern conservation in phylogenetically-related plants (potato, tobacco and pepper) to obtain lists of putative functionally-related genes. The lists are then analyzed for Gene Ontology keyword enrichment. The web server ORTom has been implemented to make the results publicly-available and searchable. Few biological examples on how the tool can be used are presented.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Turin, Italy.
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Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J. Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 2010; 62:960-976. [PMID: 20230504 DOI: 10.1111/j.1365-313x.2010.04208.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.
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Affiliation(s)
- Vitantonio Pantaleo
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
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34
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Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J. Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 2010; 62:960-76. [PMID: 20230504 DOI: 10.1111/j.0960-7412.2010.04208.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.
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Affiliation(s)
- Vitantonio Pantaleo
- Istituto di Virologia Vegetale, Consiglio Nazionale delle Ricerche, Torino, Italy
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35
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Catoni M, Miozzi L, Fiorilli V, Lanfranco L, Accotto GP. Comparative analysis of expression profiles in shoots and roots of tomato systemically infected by Tomato spotted wilt virus reveals organ-specific transcriptional responses. Mol Plant Microbe Interact 2009; 22:1504-13. [PMID: 19888816 DOI: 10.1094/mpmi-22-12-1504] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tomato (Solanum lycopersicon), a model species for the family Solanaceae, is severely affected by Tomato spotted wilt virus (TSWV) worldwide. To elucidate the systemic transcriptional response of plants to TSWV infection, microarray experiments were performed on tomato. Parallel analysis of both shoots and roots revealed organ-specific responses, although the virus was present in similar concentration. In the shoots, genes related to defense and to signal transduction were induced, while there was general repression of genes related to primary and secondary metabolism as well as to amino acid metabolism. In roots, expression of genes involved in primary metabolism and signal transduction appear unaffected by TSWV infection, while those related to the response to biotic stimuli were induced and those associated to the response to abiotic stress were generally repressed or unaltered. Genes related to amino acid metabolism were unaffected, except for those involved in synthesis of secondary compounds, where induction was evident. Differential expression of genes involved in metabolism and response to ethylene and abscisic acid was observed in the two organs. Our results provide new insight into the biology of the economically important interaction between tomato and TSWV.
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Affiliation(s)
- Marco Catoni
- Institute of Plant Virology, Consiglio Nazionale delle Ricerche, Strada delle Cacce 73, Turin, Italy
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36
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Fiorilli V, Catoni M, Miozzi L, Novero M, Accotto GP, Lanfranco L. Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus. New Phytol 2009; 184:975-87. [PMID: 19765230 DOI: 10.1111/j.1469-8137.2009.03031.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
*Arbuscular mycorrhizal symbiosis develops in roots; extensive cellular reorganizations and specific metabolic changes occur, which are mirrored by local and systemic changes in the transcript profiles. *A TOM2 microarray (c. 12 000 probes) has been used to obtain an overview of the transcriptional changes that are triggered in Solanum lycopersicum roots and shoots, as a result of colonization by the arbuscular mycorrhizal fungus Glomus mosseae. The cell-type expression profile of a subset of genes was monitored, using laser microdissection, to identify possible plant determinants of arbuscule development,. *Microarrays revealed 362 up-regulated and 293 down-regulated genes in roots. Significant gene modulation was also observed in shoots: 85 up- and 337 down-regulated genes. The most responsive genes in both organs were ascribed to primary and secondary metabolism, defence and response to stimuli, cell organization and protein modification, and transcriptional regulation. Six genes, preferentially expressed in arbusculated cells, were identified. *A comparative analysis only showed a limited overlap with transcript profiles identified in mycorrhizal roots of Medicago truncatula, probably as a consequence of the largely nonoverlapping probe sets on the microarray tools used. The results suggest that auxin and abscisic acid metabolism are involved in arbuscule formation and/or functioning.
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Affiliation(s)
- Valentina Fiorilli
- Dipartimento di Biologia Vegetale, Università degli Studi di Torino, Torino, Italy
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Davino S, Napoli C, Dellacroce C, Miozzi L, Noris E, Davino M, Accotto GP. Two new natural begomovirus recombinants associated with the tomato yellow leaf curl disease co-exist with parental viruses in tomato epidemics in Italy. Virus Res 2009; 143:15-23. [DOI: 10.1016/j.virusres.2009.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 03/01/2009] [Accepted: 03/02/2009] [Indexed: 11/30/2022]
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Miozzi L, Balestrini R, Bolchi A, Novero M, Ottonello S, Bonfante P. Phospholipase A2 up-regulation during mycorrhiza formation in Tuber borchii. New Phytol 2005; 167:229-38. [PMID: 15948845 DOI: 10.1111/j.1469-8137.2005.01400.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
TbSP1 is a secreted and surface-associated phospholipase A(2) previously found to be up-regulated in C- or N-deprived free-living mycelia from the ectomycorrhizal ascomycete Tuber borchii. As nutrient limitation is considered an important environmental factor favouring the transition to symbiotic status, TbSP1 was suggested to be involved in the formation of mycorrhizas. An in vitro symbiosis system between Cistus incanus and T. borchii was set up: TbSP1 mRNA levels in free-living mycelia and in mycorrhizas sampled in different districts of the plant-fungus interaction were examined. In the same samples, TbSP1 protein expression was analysed by immunoelectron microscopy. A substantially enhanced TbSP1 mRNA expression, compared with nutrient-limited but free-living mycelia, was detected in the presence of the plant and reached maximal levels in fully developed mycorrhizas. A similar expression trend was revealed by immunolocalization experiments. We have shown that TbSP1 appears to respond to two partially overlapping yet distinct stimuli: nutrient starvation and mycorrhiza formation.
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Affiliation(s)
- Laura Miozzi
- Dipartimento di Biologia Vegetale, Università di Torino, Torino, Italy
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