Other Rice Genome Sequencing Efforts
In addition to the public rice genome sequence efforts, there have been several notable commercially-funded efforts to determine the nucleotide sequence of rice. For additional information, see the NCBI Oryza sativa (rice) genome view.
In April 2000, Monsanto was the first private company to announce a working draft of genetic map of rice (japonica type). Monsanto’s sequencing had been done under contract by universities that received both public funds and funding from Monsanto. Although Monsanto's sequencing was carried out simultaneously with the public sequencing initiative, the Monsanto data were not released to the public until June 2000, when Monsanto launched the now-defunct rice-research.org database to provide access for publicly funded researchers to its draft rice genome sequences. Shortly before Monsanto released the rice sequence data, they filed U.S. patent applications claiming more than 200,000 rice genes, promoters, and other sequences. See the Monsanto page in Chapter 10 for more information about Monsanto's patenting of the rice genome.
In January 2001, Myriad Genetics and Syngenta announced that they had also completed DNA sequencing of the entire rice genome. Excerpts from Nature News 5 April 2002:
"We can use the rice genome to help improve wheat and corn right now. The genes are interchangeable," says a member of the commercial sequencing team, Stephen Goff of the Torrey Mesa Research Institute, San Diego….
The publicly funded International Rice Genome Sequence Project, is set to deliver a complete sequence based on a slower, more expensive, but more complete, technique in 2004.
"This will be gold standard", says plant biologist Michael Bevan of the John Innes Institute, Norwich, UK. "These papers are landmarks, but they're only part of the story.”….
In the end, Syngenta has made its sequence freely available, through its own website, to non-profit institutions…
Bevan is sanguine about this arrangement. "Syngenta put a lot of resources into the project, and they need to see returns," he says. "Hopefully they will have extracted all the juice they want from the genome in a year or so and will make it fully accessible."
New Scientist (Coghlan, A., New Scientist Print Edition 14:19, 2001) also published an article about Syngenta and Myriad Genetics' sequencing project. Quote from the New Scientist article:
"Rice has become the first crop plant to have its entire genome sequenced. Syngenta, the Basel-based multinational that funded the breakthrough, expects the rice genome to unlock genetic secrets of all cereals, from wheat and barley to maize and sorghum."
3. The Rice Full-Length cDNA Consortium (National Institute of Agrobiological Sciences, RIKEN, and the Foundation for Advancement of International Science Genome Sequencing and Analysis Group
In this project, 28,469 full-length complementary DNA clones from Oryza sativa were sequenced by a consortium in Japan. The research team was led by Dr. Shoshi Kikuchi at the Department of Molecular Genetics, National Institute of Agrobiological Sciences in Ibaraki, Japan. The results of this sequencing effort were published in Science (Science 301:376-379, 2003). Other participants included the Foundation for Advancement of International Science Genome Sequencing and Analysis Group, and RIKEN.
The consortium collected 3'- EST sequences of 175,642 cDNA clones from rice, clustered them into 28,469 nonredundant groups, and sequenced all representative clones from each group. Through homology searches, they assigned protein functions to roughly 75.86% of the clones.
Shortly before the Science paper was published, the consortium filed a patent application claiming 28,469 cDNA sequences. Later in this landscape, we show a claim analysis of this patent application. Note, however, that any of the sequences filed earlier by Monsanto would constitute prior art against RIKEN's claims.
A related scientific publication was authored by Nagata et al. in 2004 (Mol Biol Evol. 21(10):1855-70). This publication disclosed a comparative analysis of plant and animal calcium signal transduction element using plant full-length cDNA data.
All above rice sequencing projects used Nipponbare, a cultivar of the rice subspecies japonica (Oriza sativa ssp. japonica), as the target rice cultivar. Beijing Genomics Institute, however, chose to sequence Oryza sativa ssp. indica, the major rice subspecies cultivated in China and many other Asian-pacific regions. Sequencing a different type of rice is important because it aids in understanding of the differences between different rice species.
BGI's sequencing project was initiated in May 2000, and used 93-11, a cultivar of Oryza sativa L. ssp. indica, as target material. This particular cultivar of indica is the paternal cultivar of a "super" hybrid rice breed called Liang-You-Pei-Jiu or LYP9, which has 20 to 30% higher yield per hectare than the average of other rice crops in the fields. A working draft of the 93-11 genome sequence was completed in October 2001 and published in Science 296: 79-92, 2003.
BGI then launched a Rice Information System (BGI-RIS) to host the rice sequence data from 93-11. In addition, the sequence information of japonica rice from Syngenta has also been included in this system based on an agreement between BGI and Syngenta. More detailed information about BGI-RIS can be found in Nucleic Acids Research, 32: D377-D382.