1001 Genomes
A Catalog of Arabidopsis thaliana Genetic Variation
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News

February 23, 2014
Chi-2 and Seattle-0 assemblies generated by SLU are now available in the Data Center.
August 1, 2013
SHOREmap v2.1 released.
August 6, 2012
Nd-1, sequenced by Center for Biotechnology of the University of Bielefeld (CeBiTec), is now available in the Data Center. See the project page for more information.
November 29, 2011
JGI strains Bay-0 and Sha (both TAIR10) are now available in the Data Center. See the project page for more information.
November 15, 2011
JGI strains (Alc-0, Blh-1, Jea, Oy-0, Ri-0 and Sakata) are now available in the Data Center.
August 28, 2011
August 4, 2011
Accession list updated for 171 Salk strains and 180 GMI strands.
Ws-2, Tnz-1 and Strand-1 (sequenced and analyzed by the MPI and MPIZ) are now available.
May 31, 2011
Short reads in FASTQ format for 80 strains generated by the MPI are now available in the Data Center.
May 31, 2011
SNP data for 180 strains generated by the GMI are now available in the Data Center.
May 31, 2011
De novo assembly of Ler-1 using ALLPATHS-LG is available here.
>> News archive...

Welcome to the 1001 Genomes Project

The 1001 Genomes Vision

The 1001 Genomes Project, launched at the beginning of 2008, has as a goal to discover the whole-genome sequence variation in 1001 strains (accessions) of the reference plant Arabidopsis thaliana. The resulting information is paving the way for a new era of genetics that identifies alleles underpinning phenotypic diversity across the entire genome and the entire species. Each of the accessions in the 1001 Genomes project is an inbred line with seeds that are freely available from the stock centre to all our colleagues. 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 analyses enabled by this project will have broad implications for areas as diverse as evolutionary sciences, plant breeding and human genetics.

The complete genome sequences of over 80 accessions were released in early 2010 by the Max Planck Institute, and many more have been added since by the Salk Institute, the Gregor Mendel Institute and Monsanto. We are on track and for completion of the 1001 Genomes project by the end of 2013. As of June 2013, over 1001 lines have been sequenced and the final set is being analyzed.


Below are the main papers that should be cited for the different datasets:

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, published online (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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