Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151
Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Pr...
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| creator | Arrieta-Ortiz, Mario L Rodríguez-R, Luis M Pérez-Quintero, Álvaro L Poulin, Lucie Díaz, Ana C Arias Rojas, Nathalia Trujillo, Cesar Restrepo Benavides, Mariana Bart, Rebecca Boch, Jens Boureau, Tristan Darrasse, Armelle David, Perrine Dugé de Bernonville, Thomas Fontanilla, Paula Gagnevin, Lionel Guérin, Fabien Jacques, Marie-Agnès Lauber, Emmanuelle Lefeuvre, Pierre Medina, Cesar Medina, Edgar Montenegro, Nathaly Muñoz Bodnar, Alejandra Noël, Laurent D Ortiz Quiñones, Juan F Osorio, Daniela Pardo, Carolina Patil, Prabhu B Poussier, Stéphane Pruvost, Olivier Robène-Soustrade, Isabelle Ryan, Robert P Tabima, Javier Urrego Morales, Oscar G Vernière, Christian Carrere, Sébastien Verdier, Valérie Szurek, Boris Restrepo, Silvia López, Camilo Koebnik, Ralf Bernal, Adriana |
| description | Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease. |
| doi_str_mv | 10.1371/journal.pone.0079704 |
| format | Article |
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Manihotis strain CIO151</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Arrieta-Ortiz, Mario L ; Rodríguez-R, Luis M ; Pérez-Quintero, Álvaro L ; Poulin, Lucie ; Díaz, Ana C ; Arias Rojas, Nathalia ; Trujillo, Cesar ; Restrepo Benavides, Mariana ; Bart, Rebecca ; Boch, Jens ; Boureau, Tristan ; Darrasse, Armelle ; David, Perrine ; Dugé de Bernonville, Thomas ; Fontanilla, Paula ; Gagnevin, Lionel ; Guérin, Fabien ; Jacques, Marie-Agnès ; Lauber, Emmanuelle ; Lefeuvre, Pierre ; Medina, Cesar ; Medina, Edgar ; Montenegro, Nathaly ; Muñoz Bodnar, Alejandra ; Noël, Laurent D ; Ortiz Quiñones, Juan F ; Osorio, Daniela ; Pardo, Carolina ; Patil, Prabhu B ; Poussier, Stéphane ; Pruvost, Olivier ; Robène-Soustrade, Isabelle ; Ryan, Robert P ; Tabima, Javier ; Urrego Morales, Oscar G ; Vernière, Christian ; Carrere, Sébastien ; Verdier, Valérie ; Szurek, Boris ; Restrepo, Silvia ; López, Camilo ; Koebnik, Ralf ; Bernal, Adriana</creator><creatorcontrib>Arrieta-Ortiz, Mario L ; Rodríguez-R, Luis M ; Pérez-Quintero, Álvaro L ; Poulin, Lucie ; Díaz, Ana C ; Arias Rojas, Nathalia ; Trujillo, Cesar ; Restrepo Benavides, Mariana ; Bart, Rebecca ; Boch, Jens ; Boureau, Tristan ; Darrasse, Armelle ; David, Perrine ; Dugé de Bernonville, Thomas ; Fontanilla, Paula ; Gagnevin, Lionel ; Guérin, Fabien ; Jacques, Marie-Agnès ; Lauber, Emmanuelle ; Lefeuvre, Pierre ; Medina, Cesar ; Medina, Edgar ; Montenegro, Nathaly ; Muñoz Bodnar, Alejandra ; Noël, Laurent D ; Ortiz Quiñones, Juan F ; Osorio, Daniela ; Pardo, Carolina ; Patil, Prabhu B ; Poussier, Stéphane ; Pruvost, Olivier ; Robène-Soustrade, Isabelle ; Ryan, Robert P ; Tabima, Javier ; Urrego Morales, Oscar G ; Vernière, Christian ; Carrere, Sébastien ; Verdier, Valérie ; Szurek, Boris ; Restrepo, Silvia ; López, Camilo ; Koebnik, Ralf ; Bernal, Adriana</creatorcontrib><description>Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0079704</identifier><identifier>PMID: 24278159</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bacteria ; Bacteriology ; Bioinformatics ; Blight ; Cassava ; Cattle ; Cell walls ; Clusters ; Deoxyribonucleic acid ; DNA ; Epidemiology ; Gene sequencing ; Genes ; Genome, Bacterial - genetics ; Genomes ; Genomics ; Health aspects ; Horizontal transfer ; Horticulture ; Infection ; Life Sciences ; Loci ; Manihot ; Microbiology and Parasitology ; Minisatellite Repeats - genetics ; Nucleotide sequence ; Pathogenicity ; Pathogens ; Phylogenetics ; Phytopathology and phytopharmacy ; Plant tissues ; Plants (botany) ; Secretion ; Strains (organisms) ; Surveys ; Transfer RNA ; Vegetal Biology ; Virulence ; Virulence - genetics ; Xanthomonas axonopodis - genetics ; Xanthomonas axonopodis - pathogenicity</subject><ispartof>PloS one, 2013-11, Vol.8 (11), p.e79704-e79704</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Arrieta-Ortiz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/3.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Attribution</rights><rights>2013 Arrieta-Ortiz et al 2013 Arrieta-Ortiz et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c726t-673740c002d6a5a20802d0301cfe55ce654321b5d923eb2c99bae7d604cc87a53</citedby><cites>FETCH-LOGICAL-c726t-673740c002d6a5a20802d0301cfe55ce654321b5d923eb2c99bae7d604cc87a53</cites><orcidid>0000-0003-2645-8098 ; 0000-0002-0110-1423 ; 0000-0002-2348-0778 ; 0000-0002-2312-2073 ; 0000-0002-2205-2886 ; 0000-0002-4419-0542 ; 0000-0002-9334-5862 ; 0000-0001-5933-4476 ; 0000-0002-1808-7082 ; 0000-0001-5425-9454 ; 0000-0002-1442-917X ; 0000-0002-3557-697X ; 0000-0003-3530-8251 ; 0000-0002-2830-9830</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838355/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838355/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24278159$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.univ-reunion.fr/hal-01199314$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Arrieta-Ortiz, Mario L</creatorcontrib><creatorcontrib>Rodríguez-R, Luis M</creatorcontrib><creatorcontrib>Pérez-Quintero, Álvaro L</creatorcontrib><creatorcontrib>Poulin, Lucie</creatorcontrib><creatorcontrib>Díaz, Ana C</creatorcontrib><creatorcontrib>Arias Rojas, Nathalia</creatorcontrib><creatorcontrib>Trujillo, Cesar</creatorcontrib><creatorcontrib>Restrepo Benavides, Mariana</creatorcontrib><creatorcontrib>Bart, Rebecca</creatorcontrib><creatorcontrib>Boch, Jens</creatorcontrib><creatorcontrib>Boureau, Tristan</creatorcontrib><creatorcontrib>Darrasse, Armelle</creatorcontrib><creatorcontrib>David, Perrine</creatorcontrib><creatorcontrib>Dugé de Bernonville, Thomas</creatorcontrib><creatorcontrib>Fontanilla, Paula</creatorcontrib><creatorcontrib>Gagnevin, Lionel</creatorcontrib><creatorcontrib>Guérin, Fabien</creatorcontrib><creatorcontrib>Jacques, Marie-Agnès</creatorcontrib><creatorcontrib>Lauber, Emmanuelle</creatorcontrib><creatorcontrib>Lefeuvre, Pierre</creatorcontrib><creatorcontrib>Medina, Cesar</creatorcontrib><creatorcontrib>Medina, Edgar</creatorcontrib><creatorcontrib>Montenegro, Nathaly</creatorcontrib><creatorcontrib>Muñoz Bodnar, Alejandra</creatorcontrib><creatorcontrib>Noël, Laurent D</creatorcontrib><creatorcontrib>Ortiz Quiñones, Juan F</creatorcontrib><creatorcontrib>Osorio, Daniela</creatorcontrib><creatorcontrib>Pardo, Carolina</creatorcontrib><creatorcontrib>Patil, Prabhu B</creatorcontrib><creatorcontrib>Poussier, Stéphane</creatorcontrib><creatorcontrib>Pruvost, Olivier</creatorcontrib><creatorcontrib>Robène-Soustrade, Isabelle</creatorcontrib><creatorcontrib>Ryan, Robert P</creatorcontrib><creatorcontrib>Tabima, Javier</creatorcontrib><creatorcontrib>Urrego Morales, Oscar G</creatorcontrib><creatorcontrib>Vernière, Christian</creatorcontrib><creatorcontrib>Carrere, Sébastien</creatorcontrib><creatorcontrib>Verdier, Valérie</creatorcontrib><creatorcontrib>Szurek, Boris</creatorcontrib><creatorcontrib>Restrepo, Silvia</creatorcontrib><creatorcontrib>López, Camilo</creatorcontrib><creatorcontrib>Koebnik, Ralf</creatorcontrib><creatorcontrib>Bernal, Adriana</creatorcontrib><title>Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.</description><subject>Bacteria</subject><subject>Bacteriology</subject><subject>Bioinformatics</subject><subject>Blight</subject><subject>Cassava</subject><subject>Cattle</subject><subject>Cell walls</subject><subject>Clusters</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Epidemiology</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genome, Bacterial - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>Horizontal transfer</subject><subject>Horticulture</subject><subject>Infection</subject><subject>Life Sciences</subject><subject>Loci</subject><subject>Manihot</subject><subject>Microbiology and Parasitology</subject><subject>Minisatellite Repeats - genetics</subject><subject>Nucleotide sequence</subject><subject>Pathogenicity</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Phytopathology and phytopharmacy</subject><subject>Plant tissues</subject><subject>Plants (botany)</subject><subject>Secretion</subject><subject>Strains (organisms)</subject><subject>Surveys</subject><subject>Transfer RNA</subject><subject>Vegetal Biology</subject><subject>Virulence</subject><subject>Virulence - genetics</subject><subject>Xanthomonas axonopodis - genetics</subject><subject>Xanthomonas axonopodis - 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survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151</title><author>Arrieta-Ortiz, Mario L ; Rodríguez-R, Luis M ; Pérez-Quintero, Álvaro L ; Poulin, Lucie ; Díaz, Ana C ; Arias Rojas, Nathalia ; Trujillo, Cesar ; Restrepo Benavides, Mariana ; Bart, Rebecca ; Boch, Jens ; Boureau, Tristan ; Darrasse, Armelle ; David, Perrine ; Dugé de Bernonville, Thomas ; Fontanilla, Paula ; Gagnevin, Lionel ; Guérin, Fabien ; Jacques, Marie-Agnès ; Lauber, Emmanuelle ; Lefeuvre, Pierre ; Medina, Cesar ; Medina, Edgar ; Montenegro, Nathaly ; Muñoz Bodnar, Alejandra ; Noël, Laurent D ; Ortiz Quiñones, Juan F ; Osorio, Daniela ; Pardo, Carolina ; Patil, Prabhu B ; Poussier, Stéphane ; Pruvost, Olivier ; Robène-Soustrade, Isabelle ; Ryan, Robert P ; Tabima, Javier ; Urrego Morales, Oscar G ; Vernière, Christian ; Carrere, Sébastien ; Verdier, Valérie ; Szurek, Boris ; Restrepo, Silvia ; López, Camilo ; Koebnik, Ralf ; Bernal, Adriana</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c726t-673740c002d6a5a20802d0301cfe55ce654321b5d923eb2c99bae7d604cc87a53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Bacteria</topic><topic>Bacteriology</topic><topic>Bioinformatics</topic><topic>Blight</topic><topic>Cassava</topic><topic>Cattle</topic><topic>Cell walls</topic><topic>Clusters</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Epidemiology</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genome, Bacterial - genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Horizontal transfer</topic><topic>Horticulture</topic><topic>Infection</topic><topic>Life Sciences</topic><topic>Loci</topic><topic>Manihot</topic><topic>Microbiology and Parasitology</topic><topic>Minisatellite Repeats - genetics</topic><topic>Nucleotide sequence</topic><topic>Pathogenicity</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Phytopathology and phytopharmacy</topic><topic>Plant tissues</topic><topic>Plants (botany)</topic><topic>Secretion</topic><topic>Strains (organisms)</topic><topic>Surveys</topic><topic>Transfer RNA</topic><topic>Vegetal Biology</topic><topic>Virulence</topic><topic>Virulence - genetics</topic><topic>Xanthomonas axonopodis - genetics</topic><topic>Xanthomonas axonopodis - pathogenicity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Arrieta-Ortiz, Mario L</creatorcontrib><creatorcontrib>Rodríguez-R, Luis M</creatorcontrib><creatorcontrib>Pérez-Quintero, Álvaro L</creatorcontrib><creatorcontrib>Poulin, Lucie</creatorcontrib><creatorcontrib>Díaz, Ana C</creatorcontrib><creatorcontrib>Arias Rojas, Nathalia</creatorcontrib><creatorcontrib>Trujillo, Cesar</creatorcontrib><creatorcontrib>Restrepo Benavides, Mariana</creatorcontrib><creatorcontrib>Bart, Rebecca</creatorcontrib><creatorcontrib>Boch, Jens</creatorcontrib><creatorcontrib>Boureau, Tristan</creatorcontrib><creatorcontrib>Darrasse, Armelle</creatorcontrib><creatorcontrib>David, Perrine</creatorcontrib><creatorcontrib>Dugé de Bernonville, Thomas</creatorcontrib><creatorcontrib>Fontanilla, Paula</creatorcontrib><creatorcontrib>Gagnevin, Lionel</creatorcontrib><creatorcontrib>Guérin, Fabien</creatorcontrib><creatorcontrib>Jacques, Marie-Agnès</creatorcontrib><creatorcontrib>Lauber, Emmanuelle</creatorcontrib><creatorcontrib>Lefeuvre, Pierre</creatorcontrib><creatorcontrib>Medina, Cesar</creatorcontrib><creatorcontrib>Medina, Edgar</creatorcontrib><creatorcontrib>Montenegro, Nathaly</creatorcontrib><creatorcontrib>Muñoz Bodnar, Alejandra</creatorcontrib><creatorcontrib>Noël, Laurent D</creatorcontrib><creatorcontrib>Ortiz Quiñones, Juan F</creatorcontrib><creatorcontrib>Osorio, Daniela</creatorcontrib><creatorcontrib>Pardo, Carolina</creatorcontrib><creatorcontrib>Patil, Prabhu B</creatorcontrib><creatorcontrib>Poussier, Stéphane</creatorcontrib><creatorcontrib>Pruvost, Olivier</creatorcontrib><creatorcontrib>Robène-Soustrade, Isabelle</creatorcontrib><creatorcontrib>Ryan, Robert P</creatorcontrib><creatorcontrib>Tabima, Javier</creatorcontrib><creatorcontrib>Urrego Morales, Oscar G</creatorcontrib><creatorcontrib>Vernière, Christian</creatorcontrib><creatorcontrib>Carrere, Sébastien</creatorcontrib><creatorcontrib>Verdier, Valérie</creatorcontrib><creatorcontrib>Szurek, Boris</creatorcontrib><creatorcontrib>Restrepo, Silvia</creatorcontrib><creatorcontrib>López, Camilo</creatorcontrib><creatorcontrib>Koebnik, Ralf</creatorcontrib><creatorcontrib>Bernal, Adriana</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE 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Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Arrieta-Ortiz, Mario L</au><au>Rodríguez-R, Luis M</au><au>Pérez-Quintero, Álvaro L</au><au>Poulin, Lucie</au><au>Díaz, Ana C</au><au>Arias Rojas, Nathalia</au><au>Trujillo, Cesar</au><au>Restrepo Benavides, Mariana</au><au>Bart, Rebecca</au><au>Boch, Jens</au><au>Boureau, Tristan</au><au>Darrasse, Armelle</au><au>David, Perrine</au><au>Dugé de Bernonville, Thomas</au><au>Fontanilla, Paula</au><au>Gagnevin, Lionel</au><au>Guérin, Fabien</au><au>Jacques, Marie-Agnès</au><au>Lauber, Emmanuelle</au><au>Lefeuvre, Pierre</au><au>Medina, Cesar</au><au>Medina, Edgar</au><au>Montenegro, Nathaly</au><au>Muñoz Bodnar, Alejandra</au><au>Noël, Laurent D</au><au>Ortiz Quiñones, Juan F</au><au>Osorio, Daniela</au><au>Pardo, Carolina</au><au>Patil, Prabhu B</au><au>Poussier, Stéphane</au><au>Pruvost, Olivier</au><au>Robène-Soustrade, Isabelle</au><au>Ryan, Robert P</au><au>Tabima, Javier</au><au>Urrego Morales, Oscar G</au><au>Vernière, Christian</au><au>Carrere, Sébastien</au><au>Verdier, Valérie</au><au>Szurek, Boris</au><au>Restrepo, Silvia</au><au>López, Camilo</au><au>Koebnik, Ralf</au><au>Bernal, Adriana</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-11-22</date><risdate>2013</risdate><volume>8</volume><issue>11</issue><spage>e79704</spage><epage>e79704</epage><pages>e79704-e79704</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>24278159</pmid><doi>10.1371/journal.pone.0079704</doi><tpages>e79704</tpages><orcidid>https://orcid.org/0000-0003-2645-8098</orcidid><orcidid>https://orcid.org/0000-0002-0110-1423</orcidid><orcidid>https://orcid.org/0000-0002-2348-0778</orcidid><orcidid>https://orcid.org/0000-0002-2312-2073</orcidid><orcidid>https://orcid.org/0000-0002-2205-2886</orcidid><orcidid>https://orcid.org/0000-0002-4419-0542</orcidid><orcidid>https://orcid.org/0000-0002-9334-5862</orcidid><orcidid>https://orcid.org/0000-0001-5933-4476</orcidid><orcidid>https://orcid.org/0000-0002-1808-7082</orcidid><orcidid>https://orcid.org/0000-0001-5425-9454</orcidid><orcidid>https://orcid.org/0000-0002-1442-917X</orcidid><orcidid>https://orcid.org/0000-0002-3557-697X</orcidid><orcidid>https://orcid.org/0000-0003-3530-8251</orcidid><orcidid>https://orcid.org/0000-0002-2830-9830</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-11, Vol.8 (11), p.e79704-e79704 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1460879568 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Bacteria Bacteriology Bioinformatics Blight Cassava Cattle Cell walls Clusters Deoxyribonucleic acid DNA Epidemiology Gene sequencing Genes Genome, Bacterial - genetics Genomes Genomics Health aspects Horizontal transfer Horticulture Infection Life Sciences Loci Manihot Microbiology and Parasitology Minisatellite Repeats - genetics Nucleotide sequence Pathogenicity Pathogens Phylogenetics Phytopathology and phytopharmacy Plant tissues Plants (botany) Secretion Strains (organisms) Surveys Transfer RNA Vegetal Biology Virulence Virulence - genetics Xanthomonas axonopodis - genetics Xanthomonas axonopodis - pathogenicity |
| title | Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151 |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T16%3A37%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genomic%20survey%20of%20pathogenicity%20determinants%20and%20VNTR%20markers%20in%20the%20cassava%20bacterial%20pathogen%20Xanthomonas%20axonopodis%20pv.%20Manihotis%20strain%20CIO151&rft.jtitle=PloS%20one&rft.au=Arrieta-Ortiz,%20Mario%20L&rft.date=2013-11-22&rft.volume=8&rft.issue=11&rft.spage=e79704&rft.epage=e79704&rft.pages=e79704-e79704&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0079704&rft_dat=%3Cgale_plos_%3EA478165297%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1460879568&rft_id=info:pmid/24278159&rft_galeid=A478165297&rft_doaj_id=oai_doaj_org_article_cb872a7c94b4438ba2c3091674ac7841&rfr_iscdi=true |