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The University of North Carolina at Chapel Hill?s newest "library" is not
the kind that will entice an average book lover, but it eventually will
please thousands of plant scientists around the world. Through such
researchers? work, it will undoubtedly contribute to improving crops that
humans around the planet depend on every day, its developers say, April 2005
by David Williamson.

Named Phytome, the unique library is a compilation of voluminous genetic
data on 39 plant species. The list includes almost all the world?s most
valuable crops, among them rice, wheat, corn and potatoes.

"But it?s also much more than just a repository of genetic information,"
said Dr. Todd J. Vision, assistant professor of biology in UNC?s College of
Arts and Sciences.

"It allows plant researchers to ask complex questions that involve
comparisons across different genes and species, such as ?what genes with
known function are related to this gene with unknown function?? or ?what
biochemical functions have been gained or lost in different species,?"
Vision said.

Answers to those kinds of questions will lead to plants that yield more food
and resist damage from diseases and insects more successfully, he said. They
also can lead to better and cheaper medicines and plant products like
cotton, paper and rubber.

"A persistent challenge of genomics is how to capture, analyze and
distribute the massive amounts of data being churned out at record levels
from ongoing genome projects," he said. "Creating useful and accessible
tools like this is critical to the field. Even if researchers have access to
all the genomic data and all the methods necessary to analyze it, it takes a
lot of human and computer effort to put those two things together in one
user-friendly package like Phytome."

Phytome went online at www.phytome.org in the fall after two years work and
already is being used by basic and applied scientists worldwide. The first
version of the database contains information on more than 730,000 unique
protein sequences in more than 25,000 protein families.

Analysis of that data required 460 days of computer processing time, but it
was condensed into a few short weeks by use of parallel computing, Vision
said.

Currently, scientists know the complete genetic makeup of only a handful of
plants although humans are economically dependent on dozens of different
ones, he said. It would be far too expensive and time-consuming, however, to
characterize the genomes of all of them experimentally.

"Many plants are impractical to work with experimentally because they have
genomes full of material that serves no known function," Vision said. "For
example, the lily genome is roughly 40 times the size of the human genome."

Nevertheless, the gene content of lilies can be predicted reasonably well by
looking at a related plant with a small genome, like rice, he said. To breed
better crops, it?s important to be able to leverage the information from the
tractable model systems that scientists already know so much about.

"We will continue to add new features to Phytome over the next few years,"
Vision said. "Perhaps the most important will be the ability to compare the
genetic maps of multiple species simultaneously and predict the gene content
in regions of plant genomes that have not yet been deciphered."

Besides Vision, others involved in the development of Phytome are Dr.
Stefanie Hartmann, a postdoctoral researcher in biology; Dihui Lu, a
graduate student in information and library science; and computer programmer
Jason Phillips.

The National Science Foundation is supporting the project with a five-year,
$1 million grant it awarded to UNC in 2002.

"This is a unique resource for scientists trying to understand the genes
contributing to variation in traits of economic importance in crops," Vision
said.

[www.unc.edu]

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