1001 Genomes

A Catalog of Arabidopsis thaliana Genetic Variation.


Explore the variants. We maintain several tools for data download, visualization, and analysis.



Visit the Data Center and download whole sets of SNPs, indels, SVs, and genome sequences.


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.

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The main publication for the 1001 Genomes Project:

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana
1001 Genomes Consortium
Cell (2016), 166(2) 481-91.

Papers that described subsets were:

Sequencing of natural strains of Arabidopsis thaliana with short reads
Ossowski S., Schneeberger K., Clark R. M., Lanz C., Warthmann N. and Weigel D.
Genome Res (2008), 18(12) 2024-33.
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
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.
Proc Natl Acad Sci U S A (2011), 108(25) 10249-54.
Whole-genome sequencing of multiple Arabidopsis thaliana populations
Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., Wang X., Ott F., Muller J., Alonso-Blanco C., Borgwardt K., Schmid K. J. and Weigel D.
Nat Genet (2011), 43(10) 956-63.
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M.
Nat Genet (2013) 45, 884–890
Patterns of population epigenomic diversity.
Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR.
Nature (2013) 495, 193–198
Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature (2011) 477, 419–423