1001 Genome-Project: On the way to a complete catalog of the Arabidopsis genome

But how do these variations interact at the molecular level and what changes do they cause in the gene products? The computational biologist Gunnar Rätsch from the Friedrich Miescher Laboratory examined these questions in detail in a second study together with his international colleagues. They analyzed 19 strains of Arabidopsis with a particularly large genetic variability. These 19 individuals formed the basis of an artificial population of several hundred strains, created through multiple crosses such that different genome segments were shuffled systematically. The resulting individuals are ideally suited for examining gene interactions. The scientists studied the genome segments using novel analysis methods of analysis and discovered in detail how DNA is read in detail and how the intermediate stage of protein production, the RNA, is produced.

The researchers obtained detailed insight into the altered gene products arising from the various genomic variants. Depending on the genomic context some gene segments were either shut down or reactivated. "We can find a surprising number of changes affecting a single gene. However, they are often compensated for and therefore often have no significant effect on the gene products," says Gunnar Rätsch about the new results. The concepts, methods and platforms developed based on the genomic variation of Arabidopsis thaliana can also be used to study crop plants and for fast and accurate mapping of desirable characteristics. In addition, researchers can transfer this understanding about the influence of variation on gene products and their interactions to studies of the human genome.

These new projects should be viewed in the context of the 1001 Genomes Project, which was launched in 2008 at the Max Planck Institute for Developmental Biology and is being implemented through many individual projects in cooperation with ten other institutions worldwide. The aim is to analyze and compare the genes of 1001 different Arabidopsis strains. The goal of this large-scale project is to obtain fundamental insights into evolution, genetics and molecular mechanisms. Almost 500 different genomes have already been sequenced and analyzed at the different institutions. The data is being fed into a public database, which can be accessed not only by participants of the projects, but by all interested scientists.

More information:

Cao, J., Schneeberger, K., Ossowski, S., Günther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Müller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K. J., and Weigel, D. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics, doi: 10.1038/ng.911

Gan X., Stegle O., Behr J., Steffen J.G., Drewe P., Hildebrand K.L., Lyngsoe R., Schultheiss S.J., Osborne E.J., Sreedharan V.T., Kahles A., Bohnert R., Jean G., Derwent P., Kersey P., Belfield E.J., Harberd N.P., Kemen E., Toomajian C., Kover P.X., Clark R.M., Rätsch G., Mott R. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, doi: 10.1038/nature10414

Schneeberger, K., Ossowski, S., Ott, F., Klein, J. D., Wang, X., Lanz, C., Smith, L. M., Cao, J., Fitz, J., Warthmann, N., Henz, S. R., Huson, D. H., and Weigel, D. (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proceedings of the National Academy of Sciences of USA 108, 10249-10254, doi: 10.1073/pnas.1107739108

Provided by Max-Planck-Gesellschaft