1
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Baekelandt A, Saltenis VLR, Nacry P, Malyska A, Cornelissen M, Nanda AK, Nair A, Rogowsky P, Pauwels L, Muller B, Collén J, Blomme J, Pribil M, Scharff LB, Davies J, Wilhelm R, Rolland N, Harbinson J, Boerjan W, Murchie EH, Burgess AJ, Cohan J, Debaeke P, Thomine S, Inzé D, Lankhorst RK, Parry MAJ. Paving the way towards future‐proofing our crops. Food Energy Secur 2023. [DOI: 10.1002/fes3.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Vandasue L. R. Saltenis
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Philippe Nacry
- BPMP, Univ. Montpellier, INRAE, CNRS, Institut Agro Montpellier France
| | | | | | - Amrit Kaur Nanda
- Plants for the Future' European Technology Platform Brussels Belgium
| | - Abhishek Nair
- Marketing and Consumer Behaviour Group Wageningen University Wageningen Gelderland Netherlands
| | - Peter Rogowsky
- INRAE, UMR Plant Reproduction and Development Lyon France
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Bertrand Muller
- Université de Montpellier – LEPSE – INRAE – Institut Agro Montpellier France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Jonas Blomme
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
- Phycology Research Group, Department of Biology Ghent University Ghent Belgium
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Jessica Davies
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology Julius Kühn‐Institut – Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale Univ. Grenoble Alpes, INRAE, CNRS, CEA Grenoble France
| | - Jeremy Harbinson
- Laboratory of Biophysics Wageningen University & Research Wageningen The Netherlands
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Erik H. Murchie
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | - Alexandra J. Burgess
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | | | | | - Sébastien Thomine
- Institute for Integrative Biology of the Cell (I2BC) Université Paris‐Saclay, CEA, CNRS Gif‐sur‐Yvette France
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
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2
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Burgess AJ, Masclaux‐Daubresse C, Strittmatter G, Weber APM, Taylor SH, Harbinson J, Yin X, Long S, Paul MJ, Westhoff P, Loreto F, Ceriotti A, Saltenis VLR, Pribil M, Nacry P, Scharff LB, Jensen PE, Muller B, Cohan J, Foulkes J, Rogowsky P, Debaeke P, Meyer C, Nelissen H, Inzé D, Klein Lankhorst R, Parry MAJ, Murchie EH, Baekelandt A. Improving crop yield potential: Underlying biological processes and future prospects. Food Energy Secur 2022; 12:e435. [PMID: 37035025 PMCID: PMC10078444 DOI: 10.1002/fes3.435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant-derived products. In the coming years, plant-based research will be among the major drivers ensuring food security and the expansion of the bio-based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.
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Affiliation(s)
- Alexandra J. Burgess
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | | | - Günter Strittmatter
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS) Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS) Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | | | - Jeremy Harbinson
- Laboratory for Biophysics Wageningen University and Research Wageningen The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences Wageningen University & Research Wageningen The Netherlands
| | - Stephen Long
- Lancaster Environment Centre Lancaster University Lancaster UK
- Plant Biology and Crop Sciences University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | | | - Peter Westhoff
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS) Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, National Research Council of Italy (CNR), Rome, Italy and University of Naples Federico II Napoli Italy
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology National Research Council (CNR) Milan Italy
| | - Vandasue L. R. Saltenis
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Copenhagen Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Copenhagen Denmark
| | - Philippe Nacry
- BPMP, Univ Montpellier, INRAE, CNRS Institut Agro Montpellier France
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Copenhagen Denmark
| | - Poul Erik Jensen
- Department of Food Science University of Copenhagen Copenhagen Denmark
| | - Bertrand Muller
- Université de Montpellier ‐ LEPSE – INRAE Institut Agro Montpellier France
| | | | - John Foulkes
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | - Peter Rogowsky
- INRAE UMR Plant Reproduction and Development Lyon France
| | | | - Christian Meyer
- IJPB UMR1318 INRAE‐AgroParisTech‐Université Paris Saclay Versailles France
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
| | | | - Erik H. Murchie
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
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3
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Baekelandt A, Saltenis VLR, Pribil M, Nacry P, Harbinson J, Rolland N, Wilhelm R, Davies J, Inzé D, Parry MAJ, Klein Lankhorst R. CropBooster‐P
: Towards a roadmap for plant research to future‐proof crops in Europe. Food Energy Secur 2022. [DOI: 10.1002/fes3.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Vandasue L. R. Saltenis
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Copenhagen Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Copenhagen Denmark
| | - Philippe Nacry
- BPMP, Univ Montpellier, INRAE, CNRS, Montpellier SupAgro Montpellier France
| | - Jeremy Harbinson
- Laboratory of Biophysics Wageningen University & Research Wageningen The Netherlands
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale Univ. Grenoble Alpes, INRAE, CNRS, CEA Grenoble France
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology Julius Kühn‐Institut ‐ Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Jessica Davies
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | | | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
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4
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Gojon A, Nussaume L, Luu DT, Murchie EH, Baekelandt A, Rodrigues Saltenis VL, Cohan J, Desnos T, Inzé D, Ferguson JN, Guiderdonni E, Krapp A, Klein Lankhorst R, Maurel C, Rouached H, Parry MAJ, Pribil M, Scharff LB, Nacry P. Approaches and determinants to sustainably improve crop production. Food Energy Secur 2022. [DOI: 10.1002/fes3.369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Alain Gojon
- BPMP Institut Agro Univ Montpellier INRAE CNRS Montpellier France
| | - Laurent Nussaume
- UMR7265 Laboratoire de Biologie du Développement des Plantes Service de Biologie Végétale et de Microbiologie Environnementales Institut de Biologie Environnementale et Biotechnologie CNRS‐CEA‐Université Aix‐Marseille Saint‐Paul‐lez‐Durance France
| | - Doan T. Luu
- BPMP Institut Agro Univ Montpellier INRAE CNRS Montpellier France
| | - Erik H. Murchie
- School of Biosciences University of Nottingham Loughborough UK
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | | | | | - Thierry Desnos
- UMR7265 Laboratoire de Biologie du Développement des Plantes Service de Biologie Végétale et de Microbiologie Environnementales Institut de Biologie Environnementale et Biotechnologie CNRS‐CEA‐Université Aix‐Marseille Saint‐Paul‐lez‐Durance France
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - John N. Ferguson
- School of Biosciences University of Nottingham Loughborough UK
- Department of Plant Sciences University of Cambridge Cambridge UK
| | | | - Anne Krapp
- Institut Jean‐Pierre Bourgin INRAE AgroParisTech Université Paris‐Saclay Versailles France
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
| | | | - Hatem Rouached
- BPMP Institut Agro Univ Montpellier INRAE CNRS Montpellier France
- Department of Plant, Soil, and Microbial Sciences Michigan State University East Lansing Michigan USA
| | | | - Mathias Pribil
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Lars B. Scharff
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Philippe Nacry
- BPMP Institut Agro Univ Montpellier INRAE CNRS Montpellier France
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5
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Scharff LB, Saltenis VLR, Jensen PE, Baekelandt A, Burgess AJ, Burow M, Ceriotti A, Cohan J, Geu‐Flores F, Halkier BA, Haslam RP, Inzé D, Klein Lankhorst R, Murchie EH, Napier JA, Nacry P, Parry MAJ, Santino A, Scarano A, Sparvoli F, Wilhelm R, Pribil M. Prospects to improve the nutritional quality of crops. Food Energy Secur 2021. [DOI: 10.1002/fes3.327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Lars B. Scharff
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Vandasue L. R. Saltenis
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Poul Erik Jensen
- Department of Food Science University of Copenhagen Frederiksberg Denmark
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | | | - Meike Burow
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | - Aldo Ceriotti
- Institute of Agricultural Biology and Biotechnology National Research Council (CNR) Milan Italy
| | | | - Fernando Geu‐Flores
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
| | - Barbara Ann Halkier
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | | | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
| | - Erik H. Murchie
- School of Biosciences University of Nottingham Loughborough UK
| | | | - Philippe Nacry
- BPMPUniv MontpellierINRAECNRSMontpellier SupAgro Montpellier France
| | | | - Angelo Santino
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR) Lecce Italy
| | - Aurelia Scarano
- Institute of Sciences of Food Production (ISPA) National Research Council (CNR) Lecce Italy
| | - Francesca Sparvoli
- DynaMo Center Copenhagen Plant Science Centre Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology Julius Kühn‐Institut – Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Mathias Pribil
- Department of Plant and Environmental Sciences Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark
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6
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Cornelissen M, Małyska A, Nanda AK, Lankhorst RK, Parry MAJ, Saltenis VR, Pribil M, Nacry P, Inzé D, Baekelandt A. Biotechnology for Tomorrow's World: Scenarios to Guide Directions for Future Innovation. Trends Biotechnol 2020; 39:438-444. [PMID: 33162172 PMCID: PMC7577281 DOI: 10.1016/j.tibtech.2020.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022]
Abstract
Depending on how the future will unfold, today’s progress in biotechnology research has greater or lesser potential to be the basis of subsequent innovation. Tracking progress against indicators for different future scenarios will help to focus, emphasize, or de-emphasize discovery research in a timely manner and to maximize the chance for successful innovation. In this paper, we show how learning scenarios with a 2050 time horizon help to recognize the implications of political and societal developments on the innovation potential of ongoing biotechnological research. We also propose a model to further increase open innovation between academia and the biotechnology value chain to help fundamental research explore discovery fields that have a greater chance to be valuable for applied research. Identifying most relevant social, economic, and technological trends can help us understand in which direction future worlds could develop. Extrapolating long-term impact of current developments on the way we live may open avenues of biotechnology discovery research that would provide the starting basis for research and innovation addressing future needs. Maximizing innovation output in biotechnology requires a continuous cross-stakeholder interaction to timely share know–how obtained from discovery research in formats tailored to stakeholder use requirements
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Affiliation(s)
| | | | - Amrit Kaur Nanda
- Plants for the Future' European Technology Platform, Brussels, Belgium
| | | | - Martin A J Parry
- Lancaster University, Lancaster Environment Centre, Lancaster, Lancashire, UK
| | - Vandasue Rodrigues Saltenis
- Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philippe Nacry
- Biochemistry and Plant Molecular Physiology CNRS/INRAE/SupAgro/Univ. Montpellier, Montpellier, France
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology, Gent, Belgium; VIB Centre for Plant Systems Biology, Gent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology, Gent, Belgium; VIB Centre for Plant Systems Biology, Gent, Belgium
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7
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Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 2014. [PMID: 25064008 DOI: 10.1038/ng3046] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
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Affiliation(s)
- Anthony Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Federico Scossa
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per l'Orticoltura, Pontecagnano, Italy
| | - Marie E Bolger
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Florian Maumus
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Takayuki Tohge
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Hadi Quesneville
- French National Institute for Agricultural Research (INRA), UR1164 Research Unit in Genomics Info (URGI), INRA de Versailles-Grignon, Versailles, France
| | - Saleh Alseekh
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Eric A Fich
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Mariana Conte
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - Heike Keller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Korbinian Schneeberger
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Schwacke
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Itai Ofner
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Sonia Osorio
- 1] Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
| | - Saulo Alves Aflitos
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Elio Schijlen
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - José M Jiménez-Goméz
- 1] Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany. [2] INRA, UMR 1318, Institut Jean-Pierre Bourgin, Versailles, France
| | - Malgorzata Ryngajllo
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Seisuke Kimura
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Ravi Kumar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Daniel Koenig
- 1] Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany. [2] Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Lauren R Headland
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | - Roeland C H J van Ham
- 1] Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands. [2]
| | - René Klein Lankhorst
- Plant Research International, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Linyong Mao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Alexander Vogel
- Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany
| | - Borjana Arsova
- Entwicklungs und Molekularbiologie der Pflanzen, Heinrich Heine Universität, Düsseldorf, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Zhangjun Fei
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [3] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, New York, USA
| | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Fernando Carrari
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA)-Instituto Nacional de Tecnología Agropecuaria (INTA) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Castelar, Argentina
| | - James J Giovannoni
- 1] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA. [2] US Department of Agriculture Robert W. Holley Centre for Agriculture and Health, Ithaca, New York, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Björn Usadel
- 1] Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [2] Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), RWTH Aachen University, Aachen, Germany. [3] Institut für Bio- und Geowissenschaften 2 (IBG-2) Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Kema GHJ, van der Lee TAJ, Mendes O, Verstappen ECP, Lankhorst RK, Sandbrink H, van der Burgt A, Zwiers LH, Csukai M, Waalwijk C. Large-scale gene discovery in the septoria tritici blotch fungus Mycosphaerella graminicola with a focus on in planta expression. Mol Plant Microbe Interact 2008; 21:1249-1260. [PMID: 18700829 DOI: 10.1094/mpmi-21-9-1249] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The foliar disease septoria tritici blotch, caused by the fungus Mycosphaerella graminicola, is currently the most important wheat disease in Europe. Gene expression was examined under highly different conditions, using 10 expressed sequence tag libraries generated from M. graminicola isolate IPO323 using seven in vitro and three in planta growth conditions. To identify fungal clones in the interaction libraries, we developed a selection method based on hybridization with the entire genomic DNA of M. graminicola, to selectively enrich these libraries for fungal genes. Assembly of the 27,007 expressed sequence tags resulted in 9,190 unigenes, representing 5.2 Mb of the estimated 39-Mb genome size of M. graminicola. All libraries contributed significantly to the number of unigenes, especially the in planta libraries representing different stages of pathogenesis, which covered 15% of the library-specific unigenes. Even under presymptomatic conditions (5 days postinoculation), when fungal biomass is less than 5%, this method enabled us to efficiently capture fungal genes expressed during pathogenesis. Many of these genes were uniquely expressed in planta, indicating that in planta gene expression significantly differed from in vitro expression. Examples of gene discovery included a number of cell wall-degrading enzymes, a broad set of genes involved in signal transduction (n=11) and a range of ATP-binding cassette (n=20) and major facilitator superfamily transporter genes (n=12) potentially involved in protection against antifungal compounds or the secretion of pathogenicity factors. In addition, evidence is provided for a mycovirus in M. graminicola that is highly expressed under various stress conditions, in particular, under nitrogen starvation. Our analyses provide a unique window on in vitro and in planta gene expression of M. graminicola.
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Affiliation(s)
- Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands.
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9
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Chang SB, Yang TJ, Datema E, van Vugt J, Vosman B, Kuipers A, Meznikova M, Szinay D, Lankhorst RK, Jacobsen E, de Jong H. FISH mapping and molecular organization of the major repetitive sequences of tomato. Chromosome Res 2008; 16:919-33. [PMID: 18688733 DOI: 10.1007/s10577-008-1249-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 06/16/2008] [Accepted: 06/16/2008] [Indexed: 11/28/2022]
Abstract
This paper presents a bird's-eye view of the major repeats and chromatin types of tomato. Using fluorescence in-situ hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA](4), a microsatellite that also forms part of the pericentromeres, together with [GA](8), [GATA](4) and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6) nucleolar organizer region.
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Affiliation(s)
- Song-Bin Chang
- Wageningen University, Laboratory of Genetics, 6703 BD, Wageningen, The Netherlands
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van Hulten MC, Witteveldt J, Peters S, Kloosterboer N, Tarchini R, Fiers M, Sandbrink H, Lankhorst RK, Vlak JM. The white spot syndrome virus DNA genome sequence. Virology 2001; 286:7-22. [PMID: 11448154 DOI: 10.1006/viro.2001.1002] [Citation(s) in RCA: 344] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
White spot syndrome virus (WSSV) is at present a major scourge to worldwide shrimp cultivation. We have determined the entire sequence of the double-stranded, circular DNA genome of WSSV, which contains 292,967 nucleotides encompassing 184 major open reading frames (ORFs). Only 6% of the WSSV ORFs have putative homologues in databases, mainly representing genes encoding enzymes for nucleotide metabolism, DNA replication, and protein modification. The remaining ORFs are mostly unassigned, except for five, which encode structural virion proteins. Unique features of WSSV are the presence of a very long ORF of 18,234 nucleotides, with unknown function, a collagen-like ORF, and nine regions, dispersed along the genome, each containing a variable number of 250-bp tandem repeats. The collective information on WSSV and the phylogenetic analysis on the viral DNA polymerase suggest that WSSV differs profoundly from all presently known viruses and that it is a representative of a new virus family.
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Affiliation(s)
- M C van Hulten
- Laboratory of Virology, Wageningen University, Binnenhaven 11, Wageningen, 6709 PD, The Netherlands
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11
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Chen X, IJkel WFJ, Tarchini R, Sun X, Sandbrink H, Wang H, Peters S, Zuidema D, Lankhorst RK, Vlak JM, Hu Z. The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome. J Gen Virol 2001; 82:241-257. [PMID: 11125177 DOI: 10.1099/0022-1317-82-1-241] [Citation(s) in RCA: 177] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleotide sequence of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) DNA genome was determined and analysed. The circular genome encompasses 131,403 bp, has a G+C content of 39.1 mol% and contains five homologous regions with a unique pattern of repeats. Computer-assisted analysis revealed 135 putative ORFs of 150 nt or larger; 100 ORFs have homologues in Autographa californica multicapsid NPV (AcMNPV) and a further 15 ORFs have homologues in other baculoviruses such as Lymantria dispar MNPV (LdMNPV), Spodoptera exigua MNPV (SeMNPV) and Xestia c-nigrum granulovirus (XcGV). Twenty ORFs are unique to HaSNPV without homologues in GenBank. Among the six previously sequenced baculoviruses, AcMNPV, Bombyx mori NPV (BmNPV), Orgyia pseudotsugata MNPV (OpMNPV), SeMNPV, LdMNPV and XcGV, 65 ORFs are conserved and hence are considered as core baculovirus genes. The mean overall amino acid identity of HaSNPV ORFs was the highest with SeMNPV and LdMNPV homologues. Other than three 'baculovirus repeat ORFs' (bro) and two 'inhibitor of apoptosis' (iap) genes, no duplicated ORFs were found. A putative ORF showing similarity to poly(ADP-ribose) glycohydrolases (parg) was newly identified. The HaSNPV genome lacks a homologue of the major budded virus (BV) glycoprotein gene, gp64, of AcMNPV, BmNPV and OpMNPV. Instead, a homologue of SeMNPV ORF8, encoding the major BV envelope protein, has been identified. GeneParityPlot analysis suggests that HaSNPV, SeMNPV and LdMNPV (group II) have structural genomic features in common and are distinct from the group I NPVs and from the granuloviruses. Cluster alignment between group I and group II baculoviruses suggests that they have a common ancestor.
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Affiliation(s)
- Xinwen Chen
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands2
- Joint-Laboratory of Invertebrate Virology, Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China1
| | - Wilfred F J IJkel
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands2
| | - Renato Tarchini
- Greenomics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands3
| | - Xiulian Sun
- Joint-Laboratory of Invertebrate Virology, Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China1
| | - Hans Sandbrink
- Greenomics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands3
| | - Hualin Wang
- Joint-Laboratory of Invertebrate Virology, Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China1
| | - Sander Peters
- Greenomics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands3
| | - Douwe Zuidema
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands2
| | - René Klein Lankhorst
- Greenomics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands3
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands2
| | - Zhihong Hu
- Joint-Laboratory of Invertebrate Virology, Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China1
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Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Düsterhöft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, Fransz P. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 2000; 408:823-6. [PMID: 11130714 DOI: 10.1038/35048507] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
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Affiliation(s)
- S Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
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13
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Weide R, van Wordragen MF, Lankhorst RK, Verkerk R, Hanhart C, Liharska T, Pap E, Stam P, Zabel P, Koornneef M. Integration of the classical and molecular linkage maps of tomato chromosome 6. Genetics 1993; 135:1175-86. [PMID: 7905845 PMCID: PMC1205748 DOI: 10.1093/genetics/135.4.1175] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In the past, a classical map of the tomato genome has been established that is based on linkage data from intraspecific Lycopersicon esculentum crosses. In addition, a high density molecular linkage map has recently been constructed using a L. esculentum x L. pennellii cross. As the respective maps only partially match, they provide limited information about the relative positions of classical and molecular markers. In this paper we describe the construction of an integrated linkage map of tomato chromosome 6 that shows the position of cDNA-, genomic DNA- and RAPD markers relative to 10 classical markers. Integration was achieved by using a L. esculentum line containing an introgressed chromosome 6 from L. pennellii in crosses to a variety of L. esculentum marker lines. In addition, an improved version of the classical linkage map is presented that is based on a combined analysis of new linkage data for 16 morphological markers and literature data. Unlike the classical map currently in use, the revised map reveals clustering of markers into three major groups around the yv, m-2 and c loci, respectively. Although crossing-over rates are clearly different when comparing intraspecific L. esculentum crosses with L. esculentum x L. pennellii crosses, the clusters of morphological markers on the classical map coincide with clusters of genomic- and cDNA-markers on the molecular map constructed by Tanksley and coworkers.
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Affiliation(s)
- R Weide
- Department of Molecular Biology, Wageningen Agricultural University, The Netherlands
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14
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Hontelez JG, Lankhorst RK, Katinakis P, van den Bos RC, van Kammen A. Characterization and nucleotide sequence of a novel gene fixW upstream of the fixABC operon in Rhizobium leguminosarum. Mol Gen Genet 1989; 218:536-44. [PMID: 2555670 DOI: 10.1007/bf00332421] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
On the Rhizobium leguminosarum PRE sym plasmid, fixABC and a novel gene fixW were identified upstream of the regulatory gene nifA. The molecular masses of FixABC, 29, 44 and 50 kDa respectively, were estimated by polyacrylamide gel electrophoresis (PAGE) and of FixW, 25 kDa, by PAGE and nucleotide sequencing. Hybridization studies using bacteroid mRNA as a probe showed that fixABC is one operon which can be transcribed independently of fixW. Nucleotide sequencing revealed that both fixW and fixA are preceded by a nif consensus promoter. The fixA promoter partly overlaps the 3'-terminal coding region of fixW, indicating that readthrough from fixW into fixA is possible. Two open reading frames, ORF71 and ORF79, precede fixW and form one operon with fixW. ORF71 contains sequences homologous to the fixA promoter and 5'-terminal coding region. One more duplication of fixA sequences was detected, also located within the sym plasmid nif/fix clusters. One duplication of fixW sequences was found. No fixW homologue could be found in other nitrogen fixing organisms except in a number of R. leguminosarum strains.
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Affiliation(s)
- J G Hontelez
- Department of Molecular Biology, Agricultural University, Wageningen, The Netherlands
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