title: Castor bean organelle genome sequencing and worldwide genetic diversity analysis.
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.
authors.affiliation: Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Maximo
authors.initials: M
authors.lastname: Rivarola
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Foster
authors.forename: Agnes P
authors.initials: AP
authors.lastname: Chan
authors.forename: Amber L
authors.initials: AL
authors.lastname: Williams
authors.forename: Danny W
authors.initials: DW
authors.lastname: Rice
authors.forename: Xinyue
authors.initials: X
authors.lastname: Liu
authors.forename: Admasu
authors.initials: A
authors.lastname: Melake-Berhan
authors.forename: Heather
authors.initials: H
authors.lastname: Huot Creasy
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: M J
authors.initials: MJ
authors.lastname: Rosovitz
authors.forename: Hoda M
authors.initials: HM
authors.lastname: Khouri
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Beckstrom-Sternberg
authors.forename: Gerard J
authors.initials: GJ
authors.lastname: Allan
authors.forename: Paul
authors.initials: P
authors.lastname: Keim
authors.forename: Jacques
authors.initials: J
authors.lastname: Ravel
authors.forename: Pablo D
authors.initials: PD
authors.lastname: Rabinowicz
mesh_terms: D001483:Base Sequence; D002367:Ricinus communis / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics; D004270:DNA, Circular / Q000737:chemistry / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D054628:Genome, Chloroplast / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast; D004270:DNA, Circular; D004272:DNA, Mitochondrial; D018744:DNA, Plant