CLEMSON, SC--The Clemson University Genomics Institute here has signed a two-year contract with the Swiss life sciences company Novartis to establish the framework for sequencing the rice genome quickly and efficiently, the institute's director, Rod Wing, told BioInform. Novartis is expected to announce the agreement this week, he said.
Wing said several factors made Clemson an attractive partner for Novartis. Last October the institute was awarded an approximately $2 million National Science Foundation grant to purchase equipment to establish a genome center. Wing said the center is anchored by a Sun Ultra-30 system. The university has also committed $27 million to constructing a biotechnology building to be occupied by 2000.
Plus, Wing said his group has expertise in making bacterial artificial chromosome (BAC) libraries--time-saving templates for genome sequencing. He said Clemson has the largest collection of plant and fungal BAC libraries in the world. "We've made most and acquired some for distribution around the world," Wing said.
Since Novartis funding at Clemson began in late February, Wing's group here has been setting up a high-throughput BAC end-sequencing laboratory. Wing explained the value of BAC libraries: "You pick a BAC of interest to sequence and compare that with the BAC end database. Immediately you are able to pick the next BAC with the least amount of overlap, which reduces the amount of sequencing," he explained.
With Novartis, the Clemson institute has made a 60,000-clone BAC library of Nipponbare rice. The sequence of the 120,000 BAC clone ends will be deposited in GenBank, and a public access Novartis-Clemson web page will be established to enable other rice genome sequencing entities to freely screen the BAC libraries.
Novartis has also contracted with Clemson to fingerprint each BAC clone using a high-resolution agarose gel electrophoresis method to establish sequence-ready contigs. "We can put the fingerprints online so everybody can look at them," Wing said.
In addition to the Novartis contract, Wing applied earlier this month for a National Science Foundation Plant Genome Initiative grant. If it is approved, he said the institute will aim to sequence 100 megabases of rice DNA over the next five years.
To help complete the project, Wing has posted 12 job openings at the institute, which currently employs a staff of about 35.
Wing explained that, although comparatively little money is dedicated in the US to a rice genome project, its importance is comparable to other seed crops. "Rice is evolutionarily related to corn, wheat, barley and sorghum, and a lot of the order of the genes has been conserved through evolution," he said. "But the size of rice genome is six times smaller than corn. Rice is 430 megabases, corn is 3,000, and wheat is 15,000." So, sequencing rice could be helpful to corn and wheat genome projects, he said.
Though Wing has had smaller collaborations with Novartis on other crops and pests before, the new rice contract will contribute to making the Clemson institute a leader in rice genome sequencing in the US, he said. "We're ahead of a lot of groups by getting the instrumentation grant and then this money from industry," he said.
The value of the contract was not disclosed, but Wing said the amount--several million dollars--"is enough to complete the project."
The Clemson University Genomics Institute is online at http://genome.clemson.edu/.