IT MAY be just a few centimetres high, but a frail weed this week became a
colossus of plant science. Arabidopsis thaliana, otherwise known as
thale cress, is now the first plant to have its genome fully sequenced.
A worldwide consortium of botanists crowned a 10-year effort by publishing
the full genome of Arabidopsis in the journal Nature. They
expect it to yield vital information on the genetic secrets of all plants,
helping scientists to transform crop plants so the world can be fed with less
harm to the environment.
“It’s a huge milestone,” says Jeff Dangl, a member of the consortium based at
the University of North Carolina in Chapel Hill, who has been studying how
Arabidopsis defends itself against plant pests. “It’s a launch pad for
understanding all plant biology, and we hope in the next 10 years or so to work
out what every plant gene does.”
Advertisement
Arabidopsis joins the elite but rapidly growing club of sequenced organisms.
Other members include the fruit fly, the nematode worm, 30 or so bacteria,
brewer’s yeast and, of course, a “working draft” of Homo sapiens.
Biologists can now compare these genomes to learn what they have in common, what
makes them different, and where their paths crossed during evolution.
So why thale cress? For a start, it’s easy to grow in the lab and doesn’t
need much space. Each plant takes just 6 weeks to grow and produce as many as
5000 seeds. Botanists can knock out genes at will, and see the consequences
within weeks. This reveals the function of the missing gene.
More importantly for genetics, the weed’s genome is unusually compact. Its
115 million pairs of nucleotide-base building blocks span five chromosomes and
include some 26,000 genes. This makes it 30 times smaller than the human genome,
and many times smaller than most plant genomes too, including those of crop
plants.
Amazingly for such a tiny genome, as much as 58 per cent of it consists of
duplicated genes. This is because when Arabidopsis evolved around 100
million years ago it merged two sets of chromosomes into one, giving duplicates
of almost every gene.
“Plants are very promiscuous internally and among relatives,” says Marc
Zabeau, a member of the consortium at the University of Ghent in Belgium. This
gene duplication is thought to help plants develop new gene functions. “It’s
like having a spare you can play around with,” Zabeau says.
Although the consortium now has the complete genome, their work is far from done
(Â鶹´«Ă˝, 2 December, p 36).
“Of the 26,000 genes, only 3000
have been experimentally studied so far,” says Mike Bevan, a key member of the
consortium at the John Innes Centre in Norwich.
But those that have been studied have already thrown up some surprises. Some
200 Arabidopsis genes have been found that resemble human genes linked
with disease. These include genes for repairing DNA—which trigger cancer
if damaged—and others linked to ageing. There’s even a counterpart of
Separation anxiety, a gene linked with behavioural disorders.
Arabidopsis also seems to have inherited a large chunk of DNA—some 800
genes—wholesale from cyanobacteria, photosynthetic microbes which
pre-dated plants. Most of these genes are vital for photosynthesis, the process
by which plants harness energy from sunlight to make their food.
But many of the genes in Arabidopsis—around 30 per
cent—are different to anything so far seen in other sequenced organisms.
Different too, are the regulatory regions—the plethora of switches and
promoters that turn genes on and off.
Already, discoveries in Arabidopsis have helped botanists to improve
crop plants. These include genes to protect wheat against disease, ripen
tomatoes and double yields of rapeseed oil.
But finding out the roles for the multitude of unknown genes won’t be easy,
explains Zabeau. In knockout experiments, duplicate genes can make life tough.
When one copy is knocked out, its unaffected doppelgänger elsewhere in the
genome steps in to do its job, making it impossible to figure out what the
knocked-out gene does. “What we see is that only 10 per cent of knockouts show
any clearly observable [features],” says Zabeau.
Knowing the entire genome might solve this problem. Researchers could
identify any copies of a gene and neutralise them all with “antisense” copies
that bind to the genes and inactivate them.
The researchers acknowledge that some environmental groups may continue to
oppose attempts to improve plants by swapping genes around. But they believe
that by identifying genes linked with important traits, it may be possible to
find wild plants already carrying the trait simply by examining their genes. The
traits could then be cross-bred into related crops without genetic engineering.
“As far as GM is concerned, the genome adds knowledge to the debate,” says
Bevan.
-
More at:
Nature (vol 408, p 796, p 816, p 820 and p 823)