1001 Genomes
A Catalog of Arabidopsis thaliana Genetic Variation
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News

April 25, 2016
New tool for extracting and downloading VCF subsets now available.
January 28, 2016
New 1001G Tools for sequence download and strain identification are now online.
May 19, 2015
Accession list updated to final set of 1135 strains.
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Welcome to the 1001 Genomes Project

The 1001 Genomes Vision

The 1001 Genomes Project was launched at the beginning of 2008 to discover detailed whole-genome sequence variation in at least 1001 strains (accessions) of the reference plant Arabidopsis thaliana. These accessions are naturally inbred lines that are products of natural selection under diverse ecological conditions, enabling a research program that links genotypes and phenotypes to fitness effects, in the laboratory and the field. Seeds from the 1001 Genomes accessions are freely available from the stock centre to anybody. Unlimited numbers of plants with identical genotype can be grown and phenotyped for each accession, in as many environments as desired, and so the sequence information we collect can be used directly in association studies at biochemical, metabolic, physiological, morphological, and whole plant-fitness levels. The 1001 Genomes resource thus has broad implications for areas as diverse as evolutionary sciences, plant breeding and human genetics.

Since 2010, several sets of genomes have been released. The first phase of the project has just been completed, with publication of a detailed analysis of 1135 genomes.


The main publication for the 1001 Genomes Project:

The 1001 Genomes Consortium (2016). 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Submitted for publication.


Papers that described subsets were:

Ossowski, S., Schneeberger, K., Clark, R.M., Lanz, C., Warthmann, N., and Weigel, D. (2008). Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. (MPIOssowski2008)

Schneeberger, K., Ossowski, S., Ott, F., Klein, J.D., Wang, X., Lanz, C., Smith, L.M., Cao, J., Fitz, J., Warthmann, N., et al. (2011). Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl. Acad. Sci. USA 108, 10249-10254. (MPISchneeberger2011)

Cao, J., Schneeberger, K., Ossowski, S., Gunther, 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 43, 956-963. (MPICao2010)

Long, Q., Rabanal, F. A., Meng, D., Huber, C. D., Farlow, A., Platzer, A., Zhang, Q., Vilhjalmsson, B. J., Korte, A., Nizhynska, V., Voronin, V., Korte, P., Sedman, L., Mandakova, T., Lysak, M. A., Seren, U., Hellmann, I., and Nordborg, M. (2013). Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nature Genetics 45, 884-890. (GMINordborg2010)

Schmitz, R. J., Schultz, M. D., Urich, M. A., Nery, J. R., Pelizzola, M., Libiger, O., Alix, A., McCosh, R. B., Chen, H., Schork, N. J., and Ecker, J. R. (2013). Patterns of population epigenomic diversity. Nature 495, 193-198. (Salk)


In addition, you can access data for the paper below at http://mus.well.ox.ac.uk/19genomes/

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., and Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419-423.


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