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A Model System
The report Kay and his colleagues published appeared at the
same time as the report of the Arabidopsis genome was
published in the journal Nature, another milestone
in the history of genomics, since Arabidopsis is the
first plant to have its full genome sequenced.
There are many reasons why this work is important. Genetic
variations between particular strains of Arabidopsis
may shed light. It may enable us to understand why some strains
of a particular plant are different than others and find ways
to use those differences to, for instance, make the plants
flower more often.
Sequencing several plant genomes will allow us to access
diversity in plants. The genetic codes of several different
species can be compared to one another in the not too distant
future, and the rice genome is right around the corner, due
to be finished some time in the next couple of years. Another
genome, the legume Lotus japonicus, is being sequenced
along with its nitrogen fixing bacteria in the interest of
uncovering the genetic basis for this cooperative nitrogen
fixing.
Such comparisons promise to be directly relevant to our
lives in many ways, not the least of which is the possibility
that we will use what we learn to boost food production. “The
danger of running out of arable land is very real,” says
Kay, “and we have to solve the problem of feeding an
rapidly increasing population in the next 10 years.”
Certain crop species may eventually be modified by incorporating
diverse plant genes into crop plant genomes so that the conditions
under which they can be grown are broader. Perhaps plants
can be made to bear fruit faster and in larger and more nutritious
yields. “Understanding plant diversity from genome sequences
is going to have a huge effect on the whole of biology,”
says Kay. “People should not put their heads in the sand.”
Arabidopsis is a good model organism for several
reasons. It is tiny and has a fast generation time, both of
which fit well in the modern tight-on-space-and-time laboratory.
It also produces an overabundance of seeds at the end of its
reproductive cycle. Finally, as a weed, Arabidopsis
is easily grown.
Plant genomics stands to benefit more than just the vegetables
of the world. As more and more genomes are solved, comparisons
across genomes will become commonplace, with discoveries in
one informing on mysteries in others.
Studies involving the circadian control of Arabidopsis
have direct relevance to studies in humans because, in theory,
genes similar to those that exhibit daily fluctuations in
another species could undergo the same sort of rhythms. The
first human circadian disorder, a mutation in the gene hPer2,
was identified this year in people with familial advanced
sleep phase syndrome, a type of insomnia. There is a similar
gene to hPer2 in Drosophila melanogaster, which
makes the fruit fly an excellent system for subsequent studies
that will not just seek to understand sleep and wake cycles
but find ways to address disorders associated with those cycles.
Likewise other human genes will no doubt find their long
lost cousins in Arabidopsis. Genetically, the tiny
Arabidopsis plants are more similar to humans than
the genomes of yeast and the nematode. There are 11,000 different
types of gene families in the Arabidopsis genome, and
many of these genes have their counterparts in humans.
With its 25,498 genes spread over some 115 million base
pairs of DNA and organized into 5 chromosomes, Arabidopsis
has a very dense genome, which Kay speculates is insurance
against the deleterious effect of mutations or genetic diversity
to combat pathogens and fungi. “Quite a large part of
this genome seems to be dedicated to combating things that
nibble on it,” he says.
Moreover, says Kay, there are remarkable similarities between
the innate immunity of plants and that of humans. A lot of
the molecules that plants use to recognize pathogens are similar
to molecules in the human body that perform tasks of innate
immunity recognition performed by phagocytes.
At the same time, there are some 8,000 other genes that
have been annotated but have no known function and no corresponding
gene in some other organisms. Only time will tell what these
genes will tell us. But Kay sees a bright future.
“The Arabidopsis genome will ultimately have
equal effect on improving the health and welfare of the population
as the human genome sequence,” he says. “I truly
believe that.”
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