On 25 February 2008, Microbe World Radio reported on the 5000 virus genome project, a research project initiated by Professor Marilyn J. Roossinck at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma. Dr. Roossinck’s objective is to use the high-throughput technology from 454 Life Sciences to obtain the sequences of the genomes of 5000 different plant viruses isolated from plants in Costa Rica.
The idea is that plant viruses are poorly understood but play important roles in nature. In the 26 January 2007 issue of Science, Dr. Roossinck and colleagues published a paper in which they described a virus that conferred the ability of a fungus and a tropical grass, in a three-way mutualistic association, to grow at high soil temperatures. When the fungus was cured of the virus, it could no longer confer heat tolerance to the grass.
The viruses that are the most well-characterized are those that cause disease in humans or plants, but Dr. Roossinck estimates that only 1% of all viruses cause disease. In previous surveys of viral genomes, most of the genes identified were completely novel, with no hits in GenBank. Hence, Dr. Roossinck believes that viral genome sequences will provide a rich source of new proteins with unknown functions.
The project is focusing initially on plants that are related to major crop species. The researchers take plant samples back to lab, isolate total nucleic acid, treat with DNase, and look for double-stranded RNA, the hallmark of 80% of plant viruses. This approach is taken because double-stranded RNA in plants is rare except for that produced by viruses. On average, about 60% of the samples yield viral dsRNA. The dsRNA is amplified to DNA by PCR using random hexamer primers and reverse transcriptase. The resulting samples are contaminated with ribosomal genes and other plant genes, but the group has succeeded in obtaining a lot of viral sequences. The group is currently working on obtaining sequence and analyzing the data.
Dr. Roossinck spoke about this project in 2007 at the Center for Biodiversity and Conservation’s Twelfth Annual Symposium at the American Museum of Natural History. The topic of the symposium was Small Matters: Microbes and their Role in Conservation.
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Video and audio presentations from the Center for Biodiversity and Conservation’s Twelfth Annual Symposium are available here.