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The chromosomes of Arabidopsis

 
 
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Arabidopsis thalania - or thale cress. A common weed providing a rapid, abundant supply of biomass, to the delight of research scientists.

Arabidopsis thaliana - a common weed familiar to researchers - became the first plant fully to unveil its secrets, when it revealed the 25 000 or so genes in its DNA. In December 1999 scientists finished sequencing two of its chromosomes - a great stride towards a full knowledge of its genome and a milestone in understanding life. In particular, plants seem to have some things in common with humans.

     

The full genetic heritage of a living being was 'read' for the first time in 1995, when scientists identified every 'letter' written in the DNA of a simple bacteria, Haemophilus influenzae. Since then several other microorganisms have revealed their genetic code, plus two model laboratory animals - the worm Caenorhabditis elegans and the famous fruit fly Drosophila melanogaster. In humans, chromosome 21 was completely sequenced in December 1999, chromosome 22 in May 2000 and one month later it was announced that 97% of the genome had been sequenced. In the plant world, Arabidopsis thalania (thale cress) is the first to divulge the secrets of its genes.

Two of its five chromosomes were fully decoded in December 1999 in a joint effort by European, Japanese and US scientists. Sequencing of the other three chromosomes was completed in the summer and the whole genome of Arabidopsis by the end of 2000.

This, the first project to sequence a higher plant completely, started in 1996 (at a time when only 10% of the genome of Arabidopsis had been sequenced). Without international collaboration it could never have borne fruit. Two networks of laboratories were set up in Europe, bringing together thirty or so partners from ten countries. Japanese and American teams joined them to form the international Arabidopsis Genome Initiative.

'European laboratories have made a major contribution to this international effort, particularly to analysing the sequences obtained. Their performance is comparable with US laboratories in terms of sequencing speed and efficiency,' explains Michael Bevan, the coordinator of one of the twin projects. 'But laboratories in the USA have greater resources and are now working on several new plant genome projects.'

The hidden riches of a weed

Why Arabidopsis? This close relation of mustard is an old favourite with research scientists. It has the advantage of possessing the shortest genome amongst the higher plants: 135 million base-pairs compared with over 2 000 million in maize and close to 3 200 million in humans. 'Arabidopsis is a plant on which research teams can agree, since it is of no agricultural or commercial interest,' points out Francis Quétier, the coordinator of the second European project at Genoscope in Evry (France). 'What is more, it grows like wild grass which guarantees a rapid, abundant supply of biomass.'
Sequencing entails randomly dividing the DNA molecule containing the genome of the plant into fragments of approximately 100 000 base-pairs which, in turn, are then further divided into sections of 3 000 base-pairs each, several hundred of which will be amplified and then sequenced (i.e. read base-pair by base-pair) at both ends. Then the scientists have to piece together this vast puzzle, finding the links between the elements. A quantity of DNA equivalent to ten times the genome was needed for this task, allowing high-precision sequencing, with a set tolerance of two errors per 10 000 base-pairs.

Unity and diversity

After four years' research, Arabidopsis has revealed almost all its 25 000 genes and their precise sequence on its five chromosomes - a first in plant biology. Scientists have been able to identify the function of a large proportion of the genes detected, by comparing them with genes previously sequenced and known from other species. 'The research into the Arabidopsis genome lays a new foundation for plant biology and this knowledge can be used directly for studying crop plants,' continues Michael Bevan. 'The genes of Arabidopsis can be used to define the functions of the genes of these plants as well. Some of them could also be inserted in them to boost yields. What is more, such comparison with the genes of other organisms confirms that all living beings have a common ancestor.'

But this vast enterprise is far from over. Around 40% of the genes in Arabidopsis bear no resemblance to other genes already characterised, whether from plants or animals, and their function is still unknown. By inactivating the genes of the plant one by one and observing the effects of absence of an individual gene on development of the plant, the researchers hope to discover which role each one plays. The European Union has allocated over 22 million euros to the Arabidopsis project and is continuing to support this work, where so much is at stake in terms of spin-offs in the new 'genome-based economy'.

 
Title
European scientists sequencing Arabidopsis (ESSA)
European sequencing project for the bottom arm the Arabidopsis chromosome III

Reference
BIO2930075 -
BIO4-CT98-0549

Programme
Biotech

Contacts
Michael Bevan
John Innes Centre, Norwich, United Kingdom
Fax : +44-60352270
E-mail : michael.bevan@bbsrc.ac.uk

Francis Quétier et Marcel Salanoubat
Genoscope, Evry, France
Fax : +33-1 60872500
E-mail : quetier@genoscope.cns.fr
salanou@genoscope.cns.fr

Partners
Network of around thirty laboratories in ten European countries (Austria, Belgium, France, Germany, Greece, Ireland, Italy, the Netherlands, Spain and the United Kingdom).
This consortium is one of the members of the Arabidopsis Genome Initiative, a partnership including laboratories from the USA and Japan.

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'The research into the Arabidopsis genome lays a new foundation for plant biology and this knowledge can be used directly for studying crop plants.'

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