The article has been updated to clarify Pablo Rabinowicz's affiliation.
NEW YORK (GenomeWeb News) – An international team led by researchers at the University of Maryland and the J. Craig Venter Institute reported in the early, online edition of Nature Biotechnology yesterday that they have sequenced a draft version of the castor bean, Ricinus communis, genome.
The castor bean is an oilseed-producing plant that's garnering attention in biofuel and biosecurity circles, as well. By sequencing the plant's genome, researchers hope to learn more about producing the plant's economically valuable oil without making a toxic protein called ricin in the process. The genome is also expected to provide insights into finding and tracking the toxin.
"We believe that the castor bean genome sequence and its annotation constitute the foundation for identifying the regulatory and metabolic networks controlling castor-oil biosynthesis," senior author Pablo Rabinowicz, a plant genomics researcher with the University of Maryland Institute for Genome Sciences and formerly with JCVI, and his colleagues wrote.""When combined with metabolomics studies, these castor bean genome resources will enable metabolic engineering for improving castor oil production in crop plants lacking ricin."
Castor beans belong to the same plant family as cassava and rubber tree and are grown as a source of castor oil — a slippery substance containing a fatty acid called ricinoleic acid.
The oil is used as a lubricant for high performance engines and in some cosmetics and medical products. Castor oil is being explored as a possible biodiesel ingredient as well, since castor beans yield high concentrations of oil and grow well in some environments where other crop plants struggle.
The plant is also of interest for those concerned with biosecurity and biodefense, since it produces the toxic ricin protein. Ricin — found at highest levels in the plant's seeds — blocks ribosome function, which in turn, inhibits translation and kills cells, Rabinowicz told GenomeWeb Daily News.
Because ricin is so toxic, especially when inhaled or given intravenously, he and his colleagues noted, researchers are looking for ways to decrease the toxicity of castor beans or produce castor oil in other plants.
Rabinowicz and his co-workers isolated nuclear DNA from castor bean seedlings and used Sanger sequencing to do paired-end sequencing of the roughly 350 million base castor bean genome to 4.6 times coverage.
After assembling the sequence using the Celera assembler and annotating it with the TIGR eukaryotic annotation pipeline, the researchers identified 31,237 predicted genes representing some 3,020 predicted families.
More than half of the genome is comprised of repeat sequences, they noted, including many repeats not previously detected in other genomes.
The researchers also looked for evidence of past genome duplications in castor bean genome. When they compared these duplication patterns with those in the grape vine, poplar, papaya, and Arabidopsis thaliana sequences, they found evidence for ancient hexaploidization — triplication of the diploid genome — in the dicot common ancestor.
"When we compare triplications [in castor bean] to other dicot genomes, we also found the triplication," Rabinowicz said, explaining that some of the plants have since undergone additional rounds of duplication.
Meanwhile, their search for genes related to those coding for the toxic protein ricin uncovered 28 genes belonging to a lectin gene family — many of which clustered together in the genome.
And while many genes in the genome are present in multiple copies, those involved in oil synthesis and related processes are found in single copies.
"There is no backup copy as many genes have," Rabinowicz said, noting that this finding has implications for metabolic engineering aimed at getting other plants to produce castor oil.
Past attempts to make castor oil in plants such as Arabidopsis have yielded much lower ricinoleic acid levels than those found in castor bean seeds, he noted.
"It's not just getting that single copy gene into a plant that will make castor oil," Rabinowicz explained. "You have to look at the metabolic network and the regulatory network that is actually ending up in the accumulation of castor oil."
With the castor oil genome in hand, researchers are planning to undertake such studies, looking, for instance, at metabolome and transcriptome patterns in the castor beans to find metabolites and regulatory networks that can be manipulated in the castor beans themselves or transplanted into other plants to try to produce ricin-free castor oil.
In addition, researchers say, the genome is expected to serve as tools for "developing improved diagnostic and forensic methods for ricin detection and cultivar identification for tracing sample origins."
For his part, Rabinowicz is keen to use the castor bean genome as a resource for studying the genome of cassava, a crop plant in the same family as castor bean that's grown in parts of the developing world. To that end, he is collaborating with members of the team that announced the completion of the draft cassava genome last year.
"That opens the possibility of comparative genomics in the family, which is an important thing," Rabinowicz said, noting that the team also hopes to get an improved genome assembly for cassava.
Data generated for the castor bean sequencing study has been submitted to GenBank and genome annotation information is also available through JCVI's Castor Bean Genome Database web site.