Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis

Autores
Rivarola, Maximo Lisandro; Foster, Jeffrey T.; Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake Berhan, Admasu; Creasy, Heather Huot; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom Sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D.
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
Fil: Rivarola, Maximo Lisandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Foster, Jeffrey T.. Northern Arizona University; Estados Unidos
Fil: Chan, Agnes P.. No especifíca;
Fil: Williams, Amber L.. Northern Arizona University; Estados Unidos
Fil: Rice, Danny W.. Indiana University; Estados Unidos
Fil: Liu, Xinyue. University of Maryland; Estados Unidos
Fil: Melake Berhan, Admasu. No especifíca;
Fil: Creasy, Heather Huot. University of Maryland; Estados Unidos
Fil: Puiu, Daniela. No especifíca;
Fil: Rosovitz, M. J.. No especifíca;
Fil: Khouri, Hoda M.. University of Maryland; Estados Unidos
Fil: Beckstrom Sternberg, Stephen M.. Northern Arizona University; Estados Unidos
Fil: Allan, Gerard J.. Northern Arizona University; Estados Unidos
Fil: Keim, Paul. Northern Arizona University; Estados Unidos
Fil: Ravel, Jacques. University of Maryland; Estados Unidos
Fil: Rabinowicz, Pablo D.. University of Maryland; Estados Unidos
Materia
Genomics
Organelle
Functional
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/192771

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oai_identifier_str oai:ri.conicet.gov.ar:11336/192771
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Castor Bean Organelle genome sequencing and worldwide genetic diversity analysisRivarola, Maximo LisandroFoster, Jeffrey T.Chan, Agnes P.Williams, Amber L.Rice, Danny W.Liu, XinyueMelake Berhan, AdmasuCreasy, Heather HuotPuiu, DanielaRosovitz, M. J.Khouri, Hoda M.Beckstrom Sternberg, Stephen M.Allan, Gerard J.Keim, PaulRavel, JacquesRabinowicz, Pablo D.GenomicsOrganelleFunctionalhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.Fil: Rivarola, Maximo Lisandro. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Foster, Jeffrey T.. Northern Arizona University; Estados UnidosFil: Chan, Agnes P.. No especifíca;Fil: Williams, Amber L.. Northern Arizona University; Estados UnidosFil: Rice, Danny W.. Indiana University; Estados UnidosFil: Liu, Xinyue. University of Maryland; Estados UnidosFil: Melake Berhan, Admasu. No especifíca;Fil: Creasy, Heather Huot. University of Maryland; Estados UnidosFil: Puiu, Daniela. No especifíca;Fil: Rosovitz, M. J.. No especifíca;Fil: Khouri, Hoda M.. University of Maryland; Estados UnidosFil: Beckstrom Sternberg, Stephen M.. Northern Arizona University; Estados UnidosFil: Allan, Gerard J.. Northern Arizona University; Estados UnidosFil: Keim, Paul. Northern Arizona University; Estados UnidosFil: Ravel, Jacques. University of Maryland; Estados UnidosFil: Rabinowicz, Pablo D.. University of Maryland; Estados UnidosPublic Library of Science2011-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/192771Rivarola, Maximo Lisandro; Foster, Jeffrey T.; Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; et al.; Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis; Public Library of Science; Plos One; 6; 7; 7-2011; 1-91932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021743info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0021743info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:08:56Zoai:ri.conicet.gov.ar:11336/192771instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:08:56.851CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
title Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
spellingShingle Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
Rivarola, Maximo Lisandro
Genomics
Organelle
Functional
title_short Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
title_full Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
title_fullStr Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
title_full_unstemmed Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
title_sort Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis
dc.creator.none.fl_str_mv Rivarola, Maximo Lisandro
Foster, Jeffrey T.
Chan, Agnes P.
Williams, Amber L.
Rice, Danny W.
Liu, Xinyue
Melake Berhan, Admasu
Creasy, Heather Huot
Puiu, Daniela
Rosovitz, M. J.
Khouri, Hoda M.
Beckstrom Sternberg, Stephen M.
Allan, Gerard J.
Keim, Paul
Ravel, Jacques
Rabinowicz, Pablo D.
author Rivarola, Maximo Lisandro
author_facet Rivarola, Maximo Lisandro
Foster, Jeffrey T.
Chan, Agnes P.
Williams, Amber L.
Rice, Danny W.
Liu, Xinyue
Melake Berhan, Admasu
Creasy, Heather Huot
Puiu, Daniela
Rosovitz, M. J.
Khouri, Hoda M.
Beckstrom Sternberg, Stephen M.
Allan, Gerard J.
Keim, Paul
Ravel, Jacques
Rabinowicz, Pablo D.
author_role author
author2 Foster, Jeffrey T.
Chan, Agnes P.
Williams, Amber L.
Rice, Danny W.
Liu, Xinyue
Melake Berhan, Admasu
Creasy, Heather Huot
Puiu, Daniela
Rosovitz, M. J.
Khouri, Hoda M.
Beckstrom Sternberg, Stephen M.
Allan, Gerard J.
Keim, Paul
Ravel, Jacques
Rabinowicz, Pablo D.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genomics
Organelle
Functional
topic Genomics
Organelle
Functional
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
Fil: Rivarola, Maximo Lisandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Foster, Jeffrey T.. Northern Arizona University; Estados Unidos
Fil: Chan, Agnes P.. No especifíca;
Fil: Williams, Amber L.. Northern Arizona University; Estados Unidos
Fil: Rice, Danny W.. Indiana University; Estados Unidos
Fil: Liu, Xinyue. University of Maryland; Estados Unidos
Fil: Melake Berhan, Admasu. No especifíca;
Fil: Creasy, Heather Huot. University of Maryland; Estados Unidos
Fil: Puiu, Daniela. No especifíca;
Fil: Rosovitz, M. J.. No especifíca;
Fil: Khouri, Hoda M.. University of Maryland; Estados Unidos
Fil: Beckstrom Sternberg, Stephen M.. Northern Arizona University; Estados Unidos
Fil: Allan, Gerard J.. Northern Arizona University; Estados Unidos
Fil: Keim, Paul. Northern Arizona University; Estados Unidos
Fil: Ravel, Jacques. University of Maryland; Estados Unidos
Fil: Rabinowicz, Pablo D.. University of Maryland; Estados Unidos
description Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
publishDate 2011
dc.date.none.fl_str_mv 2011-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/192771
Rivarola, Maximo Lisandro; Foster, Jeffrey T.; Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; et al.; Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis; Public Library of Science; Plos One; 6; 7; 7-2011; 1-9
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/192771
identifier_str_mv Rivarola, Maximo Lisandro; Foster, Jeffrey T.; Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; et al.; Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis; Public Library of Science; Plos One; 6; 7; 7-2011; 1-9
1932-6203
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021743
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0021743
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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