Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.
Identifieur interne : 002B24 ( Main/Exploration ); précédent : 002B23; suivant : 002B25Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.
Auteurs : Simona Kraberger [Nouvelle-Zélande] ; Safaa G. Kumari [Tunisie] ; Abdelmagid A. Hamed [Soudan] ; Bruno Gronenborn [France] ; John E. Thomas [Australie] ; Murray Sharman [Australie] ; Gordon W. Harkins [Afrique du Sud] ; Brejnev M. Muhire [Afrique du Sud] ; Darren P. Martin [Afrique du Sud] ; Arvind Varsani [États-Unis]Source :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-7257 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN viral (génétique), Analyse de séquence d'ADN, Cicer (virologie), Données de séquences moléculaires, Geminiviridae (), Geminiviridae (génétique), Maladies des plantes (génétique), Maladies des plantes (virologie), Phylogénie, Recombinaison génétique, Soudan, Sélection génétique, Variation génétique.
- MESH :
- Wicri :
- geographic : Soudan.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Viral.
- geographic : Sudan.
- classification : Geminiviridae.
- genetics : Geminiviridae, Plant Diseases.
- virology : Cicer, Plant Diseases.
- Genetic Variation, Molecular Sequence Data, Phylogeny, Recombination, Genetic, Selection, Genetic, Sequence Analysis, DNA.
Abstract
In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.
DOI: 10.1016/j.meegid.2014.11.024
PubMed: 25444941
Affiliations:
- Afrique du Sud, Australie, France, Nouvelle-Zélande, Soudan, Tunisie, États-Unis
- Floride, Gouvernorat de Tunis
- Tunis
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Le document en format XML
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Muhire</name><affiliation wicri:level="1"><nlm:affiliation>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925</wicri:regionArea><wicri:noRegion>Cape Town 7925</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Darren P" sort="Martin, Darren P" uniqKey="Martin D" first="Darren P" last="Martin">Darren P. Martin</name><affiliation wicri:level="1"><nlm:affiliation>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925</wicri:regionArea><wicri:noRegion>Cape Town 7925</wicri:noRegion></affiliation></author><author><name sortKey="Varsani, Arvind" sort="Varsani, Arvind" uniqKey="Varsani A" first="Arvind" last="Varsani">Arvind Varsani</name><affiliation wicri:level="2"><nlm:affiliation>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA. Electronic address: arvind.varsani@canterbury.ac.nz.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25444941</idno><idno type="pmid">25444941</idno><idno type="doi">10.1016/j.meegid.2014.11.024</idno><idno type="wicri:Area/PubMed/Corpus">003124</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003124</idno><idno type="wicri:Area/PubMed/Curation">003028</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003028</idno><idno type="wicri:Area/PubMed/Checkpoint">003028</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">003028</idno><idno type="wicri:Area/Ncbi/Merge">002036</idno><idno type="wicri:Area/Ncbi/Curation">002036</idno><idno type="wicri:Area/Ncbi/Checkpoint">002036</idno><idno type="wicri:Area/Main/Merge">002B24</idno><idno type="wicri:Area/Main/Curation">002B24</idno><idno type="wicri:Area/Main/Exploration">002B24</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.</title><author><name sortKey="Kraberger, Simona" sort="Kraberger, Simona" uniqKey="Kraberger S" first="Simona" last="Kraberger">Simona Kraberger</name><affiliation wicri:level="1"><nlm:affiliation>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.</nlm:affiliation><country xml:lang="fr">Nouvelle-Zélande</country><wicri:regionArea>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140</wicri:regionArea><wicri:noRegion>Christchurch 8140</wicri:noRegion></affiliation></author><author><name sortKey="Kumari, Safaa G" sort="Kumari, Safaa G" uniqKey="Kumari S" first="Safaa G" last="Kumari">Safaa G. Kumari</name><affiliation wicri:level="3"><nlm:affiliation>Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis, Tunisia. Electronic address: s.kumari@cgiar.org.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Virology Laboratory, International Centre for Agricultural Research in the Dry Areas (ICARDA), Tunis</wicri:regionArea><placeName><settlement type="city">Tunis</settlement><region nuts="2">Gouvernorat de Tunis</region></placeName></affiliation></author><author><name sortKey="Hamed, Abdelmagid A" sort="Hamed, Abdelmagid A" uniqKey="Hamed A" first="Abdelmagid A" last="Hamed">Abdelmagid A. Hamed</name><affiliation wicri:level="1"><nlm:affiliation>Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani, Sudan.</nlm:affiliation><country xml:lang="fr">Soudan</country><wicri:regionArea>Plant Pathology Research Program, Agricultural Research Corporation, P.O. Box 126, Wadmedani</wicri:regionArea><wicri:noRegion>Wadmedani</wicri:noRegion></affiliation></author><author><name sortKey="Gronenborn, Bruno" sort="Gronenborn, Bruno" uniqKey="Gronenborn B" first="Bruno" last="Gronenborn">Bruno Gronenborn</name><affiliation wicri:level="1"><nlm:affiliation>Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette</wicri:regionArea><wicri:noRegion>91198 Gif sur Yvette</wicri:noRegion><wicri:noRegion>91198 Gif sur Yvette</wicri:noRegion></affiliation></author><author><name sortKey="Thomas, John E" sort="Thomas, John E" uniqKey="Thomas J" first="John E" last="Thomas">John E. Thomas</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001</wicri:regionArea><wicri:noRegion>QLD 4001</wicri:noRegion></affiliation></author><author><name sortKey="Sharman, Murray" sort="Sharman, Murray" uniqKey="Sharman M" first="Murray" last="Sharman">Murray Sharman</name><affiliation wicri:level="1"><nlm:affiliation>Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, QLD 4001</wicri:regionArea><wicri:noRegion>QLD 4001</wicri:noRegion></affiliation></author><author><name sortKey="Harkins, Gordon W" sort="Harkins, Gordon W" uniqKey="Harkins G" first="Gordon W" last="Harkins">Gordon W. Harkins</name><affiliation wicri:level="1"><nlm:affiliation>South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>South African National Bioinformatics Institute, SA Medical Research Unit for Bioinformatics Capacity Development, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535</wicri:regionArea><wicri:noRegion>Cape Town 7535</wicri:noRegion></affiliation></author><author><name sortKey="Muhire, Brejnev M" sort="Muhire, Brejnev M" uniqKey="Muhire B" first="Brejnev M" last="Muhire">Brejnev M. Muhire</name><affiliation wicri:level="1"><nlm:affiliation>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925</wicri:regionArea><wicri:noRegion>Cape Town 7925</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Darren P" sort="Martin, Darren P" uniqKey="Martin D" first="Darren P" last="Martin">Darren P. Martin</name><affiliation wicri:level="1"><nlm:affiliation>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925</wicri:regionArea><wicri:noRegion>Cape Town 7925</wicri:noRegion></affiliation></author><author><name sortKey="Varsani, Arvind" sort="Varsani, Arvind" uniqKey="Varsani A" first="Arvind" last="Varsani">Arvind Varsani</name><affiliation wicri:level="2"><nlm:affiliation>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA. Electronic address: arvind.varsani@canterbury.ac.nz.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand; Electron Microscope Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611</wicri:regionArea><placeName><region type="state">Floride</region></placeName></affiliation></author></analytic><series><title level="j">Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</title><idno type="eISSN">1567-7257</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cicer (virology)</term><term>DNA, Viral (genetics)</term><term>Geminiviridae (classification)</term><term>Geminiviridae (genetics)</term><term>Genetic Variation</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (virology)</term><term>Recombination, Genetic</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term><term>Sudan</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN viral (génétique)</term><term>Analyse de séquence d'ADN</term><term>Cicer (virologie)</term><term>Données de séquences moléculaires</term><term>Geminiviridae ()</term><term>Geminiviridae (génétique)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (virologie)</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Soudan</term><term>Sélection génétique</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Viral</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Sudan</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Geminiviridae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Geminiviridae</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN viral</term><term>Geminiviridae</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Cicer</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Cicer</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genetic Variation</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Geminiviridae</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Soudan</term><term>Sélection génétique</term><term>Variation génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Soudan</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.</div></front></TEI><affiliations><list><country><li>Afrique du Sud</li><li>Australie</li><li>France</li><li>Nouvelle-Zélande</li><li>Soudan</li><li>Tunisie</li><li>États-Unis</li></country><region><li>Floride</li><li>Gouvernorat de Tunis</li></region><settlement><li>Tunis</li></settlement></list><tree><country name="Nouvelle-Zélande"><noRegion><name sortKey="Kraberger, Simona" sort="Kraberger, Simona" uniqKey="Kraberger S" first="Simona" last="Kraberger">Simona Kraberger</name></noRegion></country><country name="Tunisie"><region name="Gouvernorat de Tunis"><name sortKey="Kumari, Safaa G" sort="Kumari, Safaa G" uniqKey="Kumari S" first="Safaa G" last="Kumari">Safaa G. Kumari</name></region></country><country name="Soudan"><noRegion><name sortKey="Hamed, Abdelmagid A" sort="Hamed, Abdelmagid A" uniqKey="Hamed A" first="Abdelmagid A" last="Hamed">Abdelmagid A. Hamed</name></noRegion></country><country name="France"><noRegion><name sortKey="Gronenborn, Bruno" sort="Gronenborn, Bruno" uniqKey="Gronenborn B" first="Bruno" last="Gronenborn">Bruno Gronenborn</name></noRegion></country><country name="Australie"><noRegion><name sortKey="Thomas, John E" sort="Thomas, John E" uniqKey="Thomas J" first="John E" last="Thomas">John E. Thomas</name></noRegion><name sortKey="Sharman, Murray" sort="Sharman, Murray" uniqKey="Sharman M" first="Murray" last="Sharman">Murray Sharman</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Harkins, Gordon W" sort="Harkins, Gordon W" uniqKey="Harkins G" first="Gordon W" last="Harkins">Gordon W. Harkins</name></noRegion><name sortKey="Martin, Darren P" sort="Martin, Darren P" uniqKey="Martin D" first="Darren P" last="Martin">Darren P. Martin</name><name sortKey="Muhire, Brejnev M" sort="Muhire, Brejnev M" uniqKey="Muhire B" first="Brejnev M" last="Muhire">Brejnev M. Muhire</name></country><country name="États-Unis"><region name="Floride"><name sortKey="Varsani, Arvind" sort="Varsani, Arvind" uniqKey="Varsani A" first="Arvind" last="Varsani">Arvind Varsani</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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