Simultaneous Completion of First Genomes of a Wild Plant

Researchers reported the simultaneous completion of the first genomes of wild Arabidopsis thaliana strains as part of the 1,001 Genomes Project.

Researchers from the Max Planck Institute for Developmental Biology (Tuebingen, Germany) recently announced the completion of the first genomes of wild strains of the flowering plant known as the thale cress or mouse-ear cress or formally A. thaliana. The entire genomes of two individuals of this species, one from Ireland, the other from Japan, have now been compared in detail. They were found to be remarkably different from each other, as Dr. Detlef Weigel and his colleagues wrote in the September 25, 2008, issue of the journal Genome Research.

This study marks the starting point of the 1,001 Genomes Project in which 1,001 individuals of the same species will be sequenced. The scientists are trying to correlate the genetic differences between the different strains with variation in the speed of plant growth and their resistance against infectious germs. These strategies could then also be applied to crop plants or trees.

Every genome is different. It is well known that the genome of apes must be different from the human genome and that both are different from the genome of a sunflower. It is only a few years ago that a huge research community produced at great cost a single human genome sequence. The hypothesis was that it would unlock all the fundamental characteristics of humans, since any differences between individuals were believed to be very slight, on the order of 0.1% of the entire genome.

Similar assumptions prevailed for other species, including thale cress A. thaliana, a model organism in plant science. It is one of the best-understood organisms on earth; however, the genetic differences that allow different strains of this plant to thrive in very different places all over the Northern hemisphere are largely unknown.

Until very recently, it was theorized that the similarity in appearance of different individuals of thale cress is correlated by a comparable level of similarity in the genetic material. "But is it really true that such subtle differences in our DNA or in that of thale cress can account for the great variation in individual traits? Is there indeed something like ‘the' genome of a species, or do have to change our point of view and focus on the genome of an individual?” asked Dr. Weigel, director of the Max Planck Institute for Development Biology.

Recent developments in the technology of DNA sequencing have reduced the cost for reading a single genome by several orders of magnitude, and this can now be accomplished within a week, instead of months or years. However, there are still few analytic tools for the surge of data produced by the new generation of sequencing machines, such as the one sold by the San Diego, CA, USA-based company Illumina. The Max Planck Institute group had to overcome a series of technical challenges to reconstruct the genome sequences of the two strains it analyzed from the relatively short snippets of sequences that the Illumina instrument delivers. But the first feasibility study has now been finished, demonstrating that even with these very short sequence reads not only point differences can be identified, but also missing or extra genetic material can be tracked down. "We are confident that our method is robust, and we have begun to sequence the genomes of 80 thale cress strains,” stated Dr. Weigel. The project could be finished by January 2009.

The study marks the start of a project on a much larger scale. Within the next two years the 1,001 Genomes project, led by Dr. Weigel, plans to sequence at least 1,001 different thale cress individuals from around the world. The hope is that equipped with this information, it will be possible to correlate genetic differences with variation in the speed with which plants grow, how much they branch, or how well they resist infectious germs. This project, in turn, will inform similar projects on crop plants, which have much larger genomes and are therefore more difficult to analyze.

While this is very promising, the task will not be completed once every individual genome is sequenced. In every cell, the genomes are packaged in different ways, allowing for different activities of the same genetic material. With the next sequencing techniques, these subtle differences can be studied as well. Thus, the 1,001 Genomes project will strip away only the first layer of variation.

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Max Planck Institute for Developmental Biology