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Kumar S, Chakravarty A, Sahoo L. Geminivirus diseases of legumes in India: current status and approaches for management. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2025; 31:41-65. [PMID: 39901958 PMCID: PMC11787143 DOI: 10.1007/s12298-024-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 10/24/2024] [Accepted: 11/11/2024] [Indexed: 02/05/2025]
Abstract
India has a large potential for producing a variety of legumes which are proficiently valued for small grower to the highest producers. Plant viruses predominate among the many factors that affect the production of legumes. In tropical and subtropical locations, begomovirus has become a significant productivity barrier for legume production with significant losses. The detection and molecular characterization of various begomoviruses species have been done with regard to phylogenetic analyses, infectivity on host plants, DNA replication, transgenic resistance, promoter analysis, and development of virus-based gene-silencing vectors using several techniques. The molecular detection of begomoviruses involves a variety of techniques, including polymerase chain reaction (PCR), using degenerate primers, reverse transcription PCR (RT-PCR), real time quantitative PCR, rolling-circle amplification PCR (RCA-PCR assay), RCA, and microarray/DNA chip. Begomovirus infections can be prevented by various methods such as by controlling vector populations, use of culture practices, developing virus-free planting materials, developing resistant varieties, following quarantine regulations, and adapting modern methods, including pathogen-derived resistance (PDR), RNA interference (RNAi)-mediated resistance and genome editing approach. This review focuses on current status of geminiviruses infecting various legumes, pathogenesis, genetic flexibility, recombination of begomovirus responsible for the wide host range, modern methods of control, including PDR, RNAi-mediated resistance, small RNA (sRNA)- mediated resistance, Engineered Nucleases, Zinc Finger nucleases, Transcriptional Activator nucleases, CRISPR/Cas9 mediated genome editing and various strategies for management of begomoviruses. The present study entails the view and understanding of different approaches for the begomovirus management which state knowledge about limiting the crop losses.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Anurabh Chakravarty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039 India
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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] [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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Bernal-Vicente A, Donaire L, Torre C, Gómez-Aix C, Sánchez-Pina MA, Juarez M, Hernando Y, Aranda MA. Small RNA-Seq to Characterize Viruses Responsible of Lettuce Big Vein Disease in Spain. Front Microbiol 2018; 9:3188. [PMID: 30622528 PMCID: PMC6309106 DOI: 10.3389/fmicb.2018.03188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/10/2018] [Indexed: 12/20/2022] Open
Abstract
The emerging lettuce big-vein disease (LBVD) is causing losses in lettuce production ranging from 30 to 70% worldwide. Several studies have associated this disease with Mirafiori lettuce big-vein virus (MiLBVV) alone or in mixed infection with lettuce big-vein associated virus (LBVaV). We used Illumina small RNA sequencing (sRNA-seq) to identify viruses present in symptomatic lettuce plants from commercial fields in Southern Spain. Data analysis using the VirusDetect tool showed the consistent presence of MiLBVV and LBVaV in diseased plants. Populations of MiLBVV and LBVaV viral small RNAs (sRNAs) were characterized, showing features essentially similar to those of other viruses, with the peculiarity of an uneven asymmetric distribution of MiLBVV virus-derived small RNAs (vsRNAs) for the different polarities of genomic RNA4 vs. RNAs1 to 3. Sanger sequencing of coat protein genes was used to study MiLBVV and LBVaV phylogenetic relationships and population genetics. The Spanish MiLBVV population was composed of isolates from three well-differentiated lineages and reflected almost all of the diversity reported for the MiLBVV species, whereas the LBVaV population showed very little genetic differentiation at the regional scale but lineage differentiation at a global geographical scale. Universal primers were used to detect and quantify the accumulation of MiLBVV and LBVaV in field samples; both symptomatic and asymptomatic plants from affected fields carried equal viral loads, with LBVaV accumulating at higher levels than MiLBVV.
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Affiliation(s)
| | - Livia Donaire
- Biology of Stress and Plant Pathology Department, CEBAS-CSIC, Murcia, Spain
| | - Covadonga Torre
- Department of Research and Development, ABIOPEP S.L., Murcia, Spain
| | | | | | - Miguel Juarez
- Plant Production and Microbiology Department, University Miguel Hernández of Elche, Orihuela, Spain
| | - Yolanda Hernando
- Department of Research and Development, ABIOPEP S.L., Murcia, Spain
| | - Miguel A. Aranda
- Biology of Stress and Plant Pathology Department, CEBAS-CSIC, Murcia, Spain
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8
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Hamza M, Tahir MN, Mustafa R, Kamal H, Khan MZ, Mansoor S, Briddon RW, Amin I. Identification of a dicot infecting mastrevirus along with alpha- and betasatellite associated with leaf curl disease of spinach (Spinacia oleracea) in Pakistan. Virus Res 2018; 256:174-182. [PMID: 30149045 DOI: 10.1016/j.virusres.2018.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/16/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
Abstract
Spinach is a common vegetable crop and very little data is available about its virus infection. Symptomatic leaves of spinach were collected during field survey. Circular DNA molecules were amplified from symptomatic samples using rolling circle amplification (RCA). After restriction analysis, presumed bands of virus and satellites were cloned, sequenced and analyzed. Analysis of sequenced RCA product revealed the presence of chickpea chlorotic dwarf virus (CpCDV; Mastrevirus). Further analyses of the cloned virus showed that strain "C" of CpCDV was present in symptomatic samples of spinach collected from field associated with vein darkening, curling and enations on leaves. Amplification of alpha- and betasatellites with universal primers was performed. CpCDV showed association with cotton leaf curl Multan betasatellite (CLCuMB) and cotton leaf curl Multan alphasatellites (CLCuMA). Infectivity analysis of CpCDV and CpCDV/CLCuMB were done in N. benthamiana using particle bombardment method and the results showed that CpCDV was able to transreplicates CLCuMB in this host. To our knowledge, this is the first report of a dicot infecting mastrevirus (CpCDV) along with CLCuMB and CLCuMA associated with leaf curl disease of spinach in Pakistan. The significance of the results is discussed.
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Affiliation(s)
- Muhammad Hamza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Nouman Tahir
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Department of Plant Pathology, Bahauddin Zakariya University, Multan, Pakistan
| | - Roma Mustafa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Hira Kamal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Zuhaib Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan.
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9
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Leonetti P, Accotto GP, Hanafy MS, Pantaleo V. Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control. FRONTIERS IN PLANT SCIENCE 2018; 9:319. [PMID: 29599788 PMCID: PMC5862823 DOI: 10.3389/fpls.2018.00319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/27/2018] [Indexed: 05/31/2023]
Abstract
Cicer arietinum L. (chickpea) is the world's fourth most widely grown pulse. Chickpea seeds are a primary source of dietary protein for humans, and chickpea cultivation contributes to biological nitrogen fixation in the soil, given its symbiotic relationship with rhizobia. Therefore, chickpea cultivation plays a pivotal role in innovative sustainable models of agro-ecosystems inserted in crop rotation in arid and semi-arid environments for soil improvement and the reduction of chemical inputs. Indeed, the arid and semi-arid tropical zones of Africa and Asia have been primary areas of cultivation and diversification. Yet, nowadays, chickpea is gaining prominence in Canada, Australia, and South America where it constitutes a main ingredient in vegetarian and vegan diets. Viruses and plant parasitic nematodes (PPNs) have been considered to be of minor and local impact in primary areas of cultivation. However, the introduction of chickpea in new environments exposes the crop to these biotic stresses, compromising its yields. The adoption of high-throughput genomic technologies, including genome and transcriptome sequencing projects by the chickpea research community, has provided major insights into genome evolution as well as genomic architecture and domestication. This review summarizes the major viruses and PPNs that affect chickpea cultivation worldwide. We also present an overview of the current state of chickpea genomics. Accordingly, we explore the opportunities that genomics, post-genomics and novel editing biotechnologies are offering in order to understand chickpea diseases and stress tolerance and to design innovative control strategies.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, Research Unit of Turin, National Research Council, Turin, Italy
| | - Moemen S. Hanafy
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
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