WEST LAFAYETTE, Ind. - A plant that became our fossil fuel and a devastating crop fungus are at the center of Purdue University genetic research aimed at developing farming and human health innovations.
The two projects are among only 25 in the country the Department of Energy's Joint Genome Institute Community Sequencing Program has approved and is supporting this year. The DOE, which spearheaded the human genome project, created the institute to provide scientists across the country with access to advanced genome sequencing equipment and expertise. Peer reviewers determine funding based on the scientific merit of each project.
Stephen Goodwin, a Purdue and USDA-Agricultural Research Service botanist, heads the project on the fungus, which causes major wheat damage worldwide. It is a member of a fungus family that spawns leaf-spotting diseases in cereal plants, citrus, bananas, strawberries and many other species.
Jo Ann Banks, also a Purdue botanist, leads the study of an ancient Christmas-tree looking plant from a family known as lycophyte that emerged more than 425 million years ago and is the living ancestor of all of today's seed-bearing flora. The earliest forms of lycophytes became the basis of our oil supply.
Scientists need to know how plants and animals have developed over the centuries in order to determine how to correct reproductive, development and growth problems, whether it's in people, animals or plants, Banks said. By sequencing the genome, or mapping where genes are on the chromosomes, researchers can begin learning the functions that each gene controls.
Lycophytes have some genes that are common ancestors to both plants and people, she said. In addition, reports from Chinese medicine say the plant Banks is studying, Selaginella moellendorffi, has some anticancer properties. Learning how this plant functions could provide disease treatments as well as ways to improve crop yields by understanding what makes some plants flower and bear fruit and vegetables.
"It's important to have different genomes of many plants and animals because comparing them helps us determine what genes do in other plants and animals, and how genes are regulated," Banks said. "It gives us an idea of how plants and animals evolved.
This also is true for other organisms such as fungi, Goodwin said.
"This fungus causes such devastating disease in wheat and is closely related to the pathogen that can destroy banana production," Goodwin said of the fungus Mycosphaerella graminicola. "By knowing the genome, we can learn about host and pathogen interaction. If we understand the mechanisms this pathogen uses to infect crops, then we may be able to control many plant diseases.
"Our long-term goal is to control as many of these diseases as possible and lower the use of fungicides."
Mycosphaerella graminicola annually causes 50 percent wheat yield loss worldwide and a $275 million loss in the U.S. wheat crop alone. Although it's believed that the fungus doesn't produce toxins that directly affect human health, some of the pathogens in related species do, Goodwin said. Learning how these toxins are made, the interaction between hosts and pathogens, and different ways pathogens enter cells, may impact plant, human and animal health.
The researchers will approach these goals by learning what genes do in both the fungus and the plant. The scientists also want to know which genes from ancient organisms still exist in modern plants and animals, and are shared with other species.
When genes are the same or similar in plants, animals and humans today to those of earlier species, it is called conservation of genes. It's already known that many genes are the same or related in many organisms, such as the pufferfish, humans, chickens and the commonly used research plant Arabidopsis.
"A lot of genes are common to plants and animals," Banks said. "Many genes involved with development overlap between plants and animals."
The lycophyte she is studying, Selaginella moellendorffi, is an early vascular plant that lacks true leaves and roots, and is seedless.
"When you fill your gas tank, you fill it with these plants," Banks said. "They dominated the Earth's flora during the era that's called the carboniferous period because that's when today's carbon-based fuel sources began developing."
More than 360 million years ago, lycophytes separated from a larger group of plants. The other branch of plants evolved into seed-bearing species with vascular leaves and root systems. A plant's vascular and root systems allow it to gather and circulate water and nutrients in the same way animals' vascular system do.
"The lycophyte Selaginella moellendorffi has some features of the very earliest vascular plants," she said. "By sequencing the whole genome, we can understand the course of the genes that make a vascular plant a vascular plant."
Goodwin will be looking for similar clues as he investigates the workings of Mycosphaerella graminicola.
"The species in this genus have a huge economic impact on many crops, but this one in particular damages wheat worldwide," Goodwin said. "It is closely related to a devastating one that attacks bananas and requires $2.5 billion worth of fungicide worldwide in the control effort."
Once the lycophyte and fungus genomes are known, the researchers will study the genes to determine what they do, how they are similar to other genes, what proteins they produce and what turns the genes on and off. Then the genes will be compared with already sequenced genes in everything from rice and the research plant Arabidopsis to humans and chickens. This information could lead to new methods to improve crops and combat human and plant diseases.
The Community Sequencing Program gives scientists worldwide access to large-scale sequencing at the Joint Genome Institute in Walnut Creek, Calif., for projects that the agency believes have significant scientific merit. Sequencing for both genome projects is expected to be completed by this summer.
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