Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis

Maximo Rivarola, Jeffrey T Foster, Agnes P. Chan, Amber L. Williams, Danny W. Rice, Xinyue Liu, Admasu Melake-Berhan, Heather Huot Creasy, Daniela Puiu, M. J. Rosovitz, Hoda M. Khouri, Stephen M Beckstrom-Sternberg, Gerard J Allan, Paul S Keim, Jacques Ravel, Pablo D. Rabinowicz

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere21743
JournalPLoS One
Volume6
Issue number7
DOIs
StatePublished - 2011

Fingerprint

Castor Bean
organelle genome
castor beans
Organelles
Genes
Genome
genetic variation
genome
Chloroplast Genome
chloroplasts
Type 2 Ribosome Inactivating Proteins
Oils
Ricin
Mitochondria
Methylation
Euphorbiaceae
ricin
Poisons
Medical applications
oils

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Rivarola, M., Foster, J. T., Chan, A. P., Williams, A. L., Rice, D. W., Liu, X., ... Rabinowicz, P. D. (2011). Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis. PLoS One, 6(7), [e21743]. https://doi.org/10.1371/journal.pone.0021743

Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis. / Rivarola, Maximo; 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 S; Ravel, Jacques; Rabinowicz, Pablo D.

In: PLoS One, Vol. 6, No. 7, e21743, 2011.

Research output: Contribution to journalArticle

Rivarola, M, Foster, JT, Chan, AP, Williams, AL, Rice, DW, Liu, X, Melake-Berhan, A, Creasy, HH, Puiu, D, Rosovitz, MJ, Khouri, HM, Beckstrom-Sternberg, SM, Allan, GJ, Keim, PS, Ravel, J & Rabinowicz, PD 2011, 'Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis', PLoS One, vol. 6, no. 7, e21743. https://doi.org/10.1371/journal.pone.0021743
Rivarola, Maximo ; 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 S ; Ravel, Jacques ; Rabinowicz, Pablo D. / Castor Bean Organelle genome sequencing and worldwide genetic diversity analysis. In: PLoS One. 2011 ; Vol. 6, No. 7.
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