By Elizabeth Pennisi
As the National Plant Genome Initiative turns 10, it is beefing up its
bioinformatics and its portfolio of sequenced crop and noncrop genomes.
In the genomics world, plants are second-class citizens. Researchers
have sequenced the DNA of hundreds of microbes and dozens of animals, yet
they have deciphered the genomes of just three plants, Arabidopsis, rice,
and poplar--four, if you count Chlamydomonas, an alga. Comparisons between
finned, legged, and feathered species have yielded tremendous insights into
the evolution of these organisms. Yet plant biologists still lack the
ability to compare the genomes of their favorite species, let alone begin to
construct a coherent history of plants. No wonder plant researchers are
complaining.

At a 6 July workshop to evaluate the 10-year-old National Plant Genome
Initiative (NPGI), experts in bioinformatics, plant breeding, and
biotechnology called for more plant genomes to be sequenced and lamented the
dearth of computational and analytical tools to evaluate genomes. Yet, at
the same time, they praised the program for its progress to date. Over the
past decade, NPGI has spent $780 million finding genes and sequencing plant
DNA. That's a drop in the bucket, compared to more than $3 billion available
from the National Human Genome Research Institute for decoding the genomes
of humans and other animals, notes Jeff Dangl of the University of North
Carolina, Chapel Hill. "Plant genomics research is a huge bang for the
buck," argues Dangl, who chairs the National Research Council panel charged
with reviewing NPGI and recommending future directions.

Congress kicked off this multiagency program in 1998. With prompting
from U.S. corn growers, it earmarked $40 million for the National Science
Foundation (NSF) to usher plants, in particular corn and other crops, into
the genomics era. Now 10 years later, NSF, with additional support from the
U.S. departments of Agriculture and Energy (DOE) and other federal agencies,
has sponsored hundreds of genome-related projects.

But researchers are clamoring for more DNA. At the meeting, Erik Legg
of Syngenta, which is based in Research Triangle Park, North Carolina,
called for more crop genomes. Eric Ward of the Two Blades Foundation in
Durham, North Carolina, which supports the development of disease-resistant
crops, cited the need for species that represent all the plant groups.
Others argued for "resequencing" species from different places whose genomes
are already known--say, Arabidopsis--to get a sense of the natural
variation.

Workshop participants also decried the genome initiative's lack of
progress in bioinformatics. Funding agencies supported the sequencing of
many animal species to help interpret the human genome. Toward that end,
centralized databases, such as Ensembl, developed ways to compare genomes
and look for conserved genes and pathways. That hasn't happened in the plant
world. As a result, "data resources are balkanized," complains Lincoln
Stein, a bioinformaticist at Cold Spring Harbor Laboratory in New York
state. For Arabidopsis sequence information, researchers go to a database
called TAIR, but for corn, they head to MaizeGDB. "[You] can't go and see a
comprehensive comparison between Arabidopsis and rice," notes Ward. "It's
frustrating."

Stein and others called for the integration of the various plant
genome databases and for the establishment of uniform standards for
characterizing genes and other DNA. "If you don't do this, your comparisons
between genomes are utterly meaningless," says Suzanna Lewis, a
bioinformaticist at Lawrence Berkeley National Laboratory in California.

NSF, DOE, and its collaborating agencies are taking steps to address
these complaints. In late 2005, NSF awarded Washington University in St.
Louis, Missouri, $29.5 million to sequence corn. Potato, tomato, and soybean
sequencing is also under way. DOE's Joint Genome Institute in Walnut Creek,
California, plans to devote increasingly more of its sequencing capacity to
plants and microbes, curtailing its work with animals, says JGI's Daniel
Rokhsar. All told, about two dozen species are in the sequencing hopper.

NSF is pushing for better bioinformatics as well. It is reviewing
proposals for a "plant cyberinfrastructure," which will have the computers
and know-how to meld the various sequence, gene-expression, functional
genomics, and mutant databases to make possible one-stop shopping for
genomics. NSF plans to spend up to $10 million a year for 5 years--10 years
at most--to make these genomic resources accessible and to train researchers
how to use them. Training is key, says Dangl. NPGI has "brought the mind
frame of genomics to plant systems where there wasn't much before," he
notes.

Indeed, NPGI has become "the major basic science program for plants,"
says Jeffrey Bennetzen of the University of Georgia, Athens. The initiative
will never have the resources of the National Human Genome Research
Institute, but it is slowly lifting plants from second-class status.


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