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Castor bean organelle genome sequencing and worldwide genetic diversity analysis

Rivarola, Maximo and Foster, Jeffrey T. and Chan, Agnes P. and Williams, Amber L. and Rice, Danny W. and Liu, Xinyue and Melake-Berhan, Admasu and Huot Creasy, Heather and Puiu, Daniela and Rosovitz, M. J. and Khouri, Hoda M. and Beckstrom-Sternberg, Stephen M. and Allan, Gerard J. and Keim, Paul and Ravel, Jacques and Rabinowicz, Pablo D. (2011) Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS ONE, 6 (7). e21743. ISSN 1932-6203

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Publisher’s or external URL: http://dx.doi.org/10.1371/journal.pone.0021743


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.

Item Type: Article
ID number or DOI: 10.1371/journal.pone.0021743
Related URLs:
Keywords: castor beans; chloroplast genome; complete nucleotide-sequence; dna-sequence; Euphorbiaceae; Evolution; fattyacids; industrial applications; land plants; maize; oilseeds; organization; phylogenetic-relationships; plant mitochondrial genomes; ricin; ricinus-communis; therapeutics
Subjects: Q Science > QH Natural history > QH426 Genetics
S Agriculture > SB Plant culture
NAU Depositing Author Academic Status: Faculty/Staff
Department/Unit: College of Engineering, Forestry, and Natural Science > Biological Sciences
Research Centers > Center for Microbial Genetics and Genomics
Date Deposited: 16 Oct 2015 17:51
URI: http://openknowledge.nau.edu/id/eprint/1699

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