Ode to the Poplar
The first complete DNA sequence of a tree, Populus trichocarpa, has been released. Known to laymen as Black Cottonwood or poplar, this forest tree is not only of interest for plant researchers but also ecologically and commercially valuable. The knowledge of its DNA sequence fulfils many a scientist's dream. By Anja Possart
They are the dominant life form in many ecosystems. They cover about 30% of the global land surface, contain more than 90% of all terrestrial biomass and provide structural and functional habitat for two-thirds of the Earth's terrestrial species. And if this wasn't enough responsibility they also undertake the tasks of carbon sequestration, watershed protection, air cleaning, etc. - the list is virtually endless. Considering their acting as jack-of-all-trades it is not surprising that forest trees are the focus of scientific interest all over the world.
As presented in the September edition of the journal
Science (Vol 313), an international consortium including amongst others the Umea Plant Science Centre, Sweden and Ghent University, Belgium has released the first complete DNA sequence of such a forest tree. With the genome of the Black Cottonwood tree,
Populus trichocarpa, the scientific community now has access to the third plant genome, right after the genomes of
Arabidopsis thaliana and Rice.
The Poplar was selected as a model forest species not only because of its relatively compact genome size but also because of its rapid growth and relative ease of experimental manipulation. With about 480 million letters of genetic code on 19 chromosomes the poplar genome has four times more base pairs than
Arabidopsis but is still some 40 times smaller than the genome of pine. Therefore, its eight-fold sequencing could be done in an appropriate time. Through the integration of shotgun sequence assembly and genetic mapping, the scientists were able to reconstruct the whole genome of a female
Populus from the banks of the Nisqually River in the state of Washington, USA. A first-draft reference set of 45,555 putative protein-coding gene loci was identified in the nuclear genome, 101 and 52 genes were annotated in the chloroplast and mitochondrial genomes, respectively. That is more genes than have been found for any other organism sequenced to date, approximately twice as many as present in the human genome.
The comparison with the genome of
Arabidopsis showed that for about 10% of the poplar genes there are no homologue genes in the old-established workhorse for plant molecular genetics. This is the first exciting step towards determining the genetic difference between trees and herbs. Although
Populus has substantially more protein-coding genes than
Arabidopsis, the relative frequency of protein domains represented in databases is similar. Noteworthy outliers in poplar include genes and gene domains which are associated with disease, insect resistance, nutrient transport and, somewhat logically, meristem development.
It is known that the lines of descent of the poplar and
Arabidopsis began to evolve in different directions some 100 to 120 million years ago. With the sequence in their hands, the researchers have determined that a doubling of a large part of the poplar's genes has occurred twice in history. The measurement of the accumulation of nucleotide divergence shed light into the age of duplicate genes. This, in turn, provided evidence of a more recent duplication event that affected roughly 92% of the genome. The first duplication happened at about the time the
Arabidopsis line of descent went its separate way.
The scientists list many more insights into non-coding RNA, tandem duplications or single-nucleotide polymorphism but we'll leave these with their
Science article for now. What is perhaps even more fascinating are the visions associated with the availability of the poplar's genome. Fundamental biological questions concerning properties of trees like, for instance, wood formation, longevity or seasonal growth can now be tackled more efficiently.
With their extraordinarily rapid growth poplars are furthermore targeted as a model crop for bio fuels production. Under optimal conditions the trees can grow a dozen feet each year and reach maturity in as few as four years. The knowledge of their complete DNA sequence now lays the groundwork that may allow the adjustment of these trees to our needs. For instance, the research team identified 93 genes associated with the production of cellulose, hemicellulose and lignin. The former can be broken down into sugars that, in turn, are fermented into alcohol and distilled to yield ethanol or other fuels.
Manipulating the genes responsible could improve growth and lignocellulosic portion supporting the scientists' visions of vast poplar farms that provide a steady supply of bio fuels. These fuels would not only cut the reliance on fossil fuels but also emit fewer pollutants - which directly leads to another possible application of a finely-tuned
Populus: the trees constitute vital managers of atmospheric carbon. They store captured carbon dioxide in their leaves, stems and roots. If one could strengthen this process and produce trees that shuttle and store more carbon in their roots, i.e. below the ground, this would improve carbon removal from the air. Moreover, burning them in the form of bio fuels won't have such far-reaching consequences as this cycle is essentially carbon neutral.
Sounds good but somehow hard to achieve? Sure, the combination of renewable energy and reduction of greenhouse gases is still in its infancy. Nevertheless, the genome sequence of
Populus trichocarpa is an extremely useful resource that will surely make the research on forest trees even more fascinating.
Link to the International Populus Genome Consortium (IPGC)
