Whole Genome Shotgun Sequencing of the Castor Bean Plant, Ricinus Communis cDNA Sequencing and Gene Annotation
The genome of Ricinus communis will be sequenced to 4X coverage, which will provide enough data to allow the assembly of the genome into a draft sequence, consisting of relatively large contigs and scaffolds. Genes and other identifiable sequences will be annotated in the assembled sequences. ESTs will also be generated during this project. These ESTs will not only allow rapid identification of genes but will also be used for genome annotation purposes. The availability of good ricin gene model information will be a great benefit to the plant scientific community.
We will use the cultivar HALE (USDA Castor Germplasm Repository at the University of Georgia, Griffith, GA - USDA-GRIN accession NSL4773), which was selected after extensive consultation with the community. The HALE cultivar available in the repository originated from Texas, USA and is the major domestically grown variety.
Background
R. communis, also known as the castor bean, is native from Africa and warmer parts of Asia. It is a perennial shrub, sometimes tree-like, ranging in size from three to fifteen feet tall. It is cultivated in many tropical and subtropical areas of the world. Castor bean has been introduced in the United States and naturalized. It is considered invasive and displaces native plant species in riparian areas and drainage. R. communis is monoecious (separate male and female flowers on the same plant), with the female flowers above the male flowers. Both kinds of flowers lack petals. R. communis is both self and cross-pollinated by wind, to varying degrees depending on the weather conditions. In wild species, seeds are ejected from the spiny seed capsule dispersing them to the ground.
R. communis is cultivated both as an oil crop and an ornamental. Depending on the size of the shrub, the number of seeds produced by a single plant varies from 1,500 to more than 150,000. A seed weights 2 to 3.5 grams. The average yields range from 300 to more than 3,000 kg of seeds per hectare. The oil content of seeds varies from 35 to 55%. Castor oil, a thick yellowish or almost colorless oil has an astonishing number of industrial and medicinal/cosmetic applications [1]. The United States are amongst the world largest importers of castor oil and its derivatives [2].
One of the problems associated with R. communis seeds is that is it highly toxic to humans, and many animals. Ricin, the toxic water-soluble protein that makes castor bean deadly, is at its highest concentration in the seeds, but is also found in the leaves. Ricin, when compared to other toxic substances, is one of the deadliest natural poisons, and most toxic when taken intravenously or inhaled as fine particles. Its biochemical activity is well characterized as a "ribosome-inactivating enzyme" or Type 2 RIP [3]. Ricin can be extracted from seeds through a relatively simple process and has been used in acts of terrorism. It has been shown that trace amount of DNA co-purifies in ricin preparations. Presently, no genotyping systems are available for R. communis, which makes it impossible to use the residual DNA to link a ricin preparation to a particular cultivar or a geographical location.
R. communis chromosomes number is 2n = 20 [4]. Autotetraploids have been produced using colchicin, and haploids have been reported, but in nature, R. communis is found mainly in the diploid form. There is little or no loss of vigor when R. communis plants are inbred [4]. The genome size has been estimated at 323 Mb [5].
Ricinus communis
| Status | Description | Date | |
| Annotation | Published | On scaffolds: EQ973772 : EQ999533 | Nov 2 2007 |
| Assembly | Published | AI 1564 | Jul 25 2006 |
| Sequence | WGS Published | AASG02000000 | Dec 27 2007 |
| Sequence | AASG02000000 | Feb 1 2007 | |
| Sequence | AASG01000000 | Jul 6 2006 | |
| Sequence | Previous WGS | AASG02000000 | Oct 17 2007 |
| Taxonomy | Available | Taxonomy ID 3988 | |
| Trace Archive | Available | 2,085,192 traces |
Progress by library
| Center Name | Genomic Library | Trace Count | Trace Type | Strategy | Insert Size | Insert Stdev |
| JCVI | 1041058381435 | 163,460 | WGS | WGA | 2,500 | 750 |
| JCVI | 1041072132107 | 240,765 | WGS | WGA | 2,500 | 750 |
| JCVI | 1041073424187 | 200,765 | WGS | WGA | 3,000 | 900 |
| JCVI | 1041074864721 | 120,562 | WGS | WGA | 33,000 | 9,900 |
| JCVI | 1041074865875 | 130,618 | WGS | WGA | 33,000 | 9,900 |
| 856,170 |
Production Status
| Organism Name | Status | Taxon | Trace | Sequence | Assembly | Annotation |
|---|---|---|---|---|---|---|
| Ricinus communis | Complete | X | T | W | A | O |
References
- Brigham, R.D. (1993) Castor: Return of an old crop. New crops (Janik, J. and Simon, J.E., Eds.), Wiley & Sons, New York.
- Roetheli, J.C., Glaser, L.K. and Brigham, R.D. (1991) Castor: Assessing the feasibility of U.S. production. USDA/CSREES, Office of Agricultural Materials. Washington, DC.
- Endo, Y., Mitsui, K., Motizuki, M. and Tsurugi, K. (1987) The mechanism of action of ricin and related toxic lectins on eukaryotic ribosomes. The site and the characteristics of the modification in 28 S ribosomal RNA caused by the toxins. J Biol Chem 262, 5908-5912. [PubMed]
- Moshkin, V.A. (1980) Castor. Kolos Publishers/American Publishing Co., Moscow.
- Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9, 211-215.