Castor bean organelle genome sequencing and worldwide genetic diversity analysis

• Published in: PloS one 2011-07, Vol.6 (7), p.e21743
• Main Authors: Rivarola, Maximo, Foster, Jeffrey T, Chan, Agnes P, Williams, Amber L, Rice, Danny W, Liu, Xinyue, Melake-Berhan, Admasu, Huot Creasy, Heather, Puiu, Daniela, Rosovitz, M J, Khouri, Hoda M, Beckstrom-Sternberg, Stephen M, Allan, Gerard J, Keim, Paul, Ravel, Jacques, Rabinowicz, Pablo D
• Format: Article
• Language: English
• Subjects: Analysis; Artificial chromosomes; Base Sequence; Bioinformatics; Biology; Biosafety; Breeding; Chloroplasts; Cladistic analysis; Deoxyribonucleic acid; DNA; DNA methylation; DNA sequencing; DNA, Chloroplast - chemistry; DNA, Chloroplast - genetics; DNA, Circular - chemistry; DNA, Circular - genetics; DNA, Mitochondrial - chemistry; DNA, Mitochondrial - genetics; DNA, Plant - chemistry; DNA, Plant - genetics; Euphorbiaceae; Evolution; Fatty acids; Forensic engineering; Forensic science; Forensic toxicology; Gene sequencing; Genetic diversity; Genetic markers; Genetic Variation; Genetics; Genome, Chloroplast - genetics; Genome, Mitochondrial - genetics; Genome, Plant - genetics; Genomes; Genomics; Genotyping; Geographical distribution; Herbal medicine; Laboratories; Lectins; Lubricants & lubrication; Markers; Medical screening; Medicine; Methylation; Molecular Sequence Data; Nucleotide sequence; Petroleum production; Phylogeny; Phylogeography; Plant breeding; Plant ecology; Polymorphism; Polymorphism, Single Nucleotide; Population genetics; Population studies; Proteins; Ribosome-inactivating protein; Ricin; Ricinus communis; Ricinus communis - classification; Ricinus communis - genetics; Ricinus communis - growth & development; Seeds; Sequence Analysis, DNA; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Species Specificity; Sulfur; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 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.