MPICao2010

80 Arabidopsis thaliana accessions

To discover sequence differences responsible for adaptation to diverse environments across the native range of Arabidopsis thaliana, we sequenced 80 wild inbred accessions from eight geographic regions in Eurasia, with 10- to 20-fold genome coverage using Illumina's sequencing-by-synthesis (SBS) technology.

Paired-end short reads (42- to 64-bp ) were analyzed using our software pipeline SHORE to identify near 5 million SNPs. In addition, we called structural variants including long insertions, deletions and inversions using paired -end information.

We have released the SNPs and structural variants (SVs) in our Data Center. We have also deposited the seeds of accessions into ABRC stock center (CS76427).

Publication


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.
Whole-genome sequencing of multiple Arabidopsis thaliana populations.
Nature Genetics 43, 956–963 (2011).

Regional distribution


We collected strains from 8 Eurasian regions:


For a higher resolution, explore the regions with Google Maps.

Accessions list


Strain Region Seq. depth Lat Long Habitat
Agu-1 N-Africa Spain 20X 41.32 -1.34 NA
Bak-2 Kaukasus 13X 41.79 43.48 open roadside
Bak-7 Kaukasus 18X 41.79 43.48 open roadside
Cdm-0 N-Africa Spain 21X 39.73 -5.74 NA
Del-10 East Europe 17X 44.94 21.18 open meadow and roadside, full sun
Dog-4 Kaukasus 11X 38.30 42.22 open, stony, grazed hillside
Don-0 N-Africa Spain 20X 36.83 -6.36 NA
Ey15-2 Tuebingen 16X 48.43 8.77 NA
Fei-0 N-Africa Spain 13X 40.92 -8.54 NA
HKT2.4 Tuebingen 19X 48.14 9.40 NA
ICE1 East Europe 15X 44.46 25.74 fallow field
ICE102 Southern Italy 18X 40.57 15.32 field margin close to shrub
ICE104 Southern Italy 22X 39.18 16.26 meadow
ICE106 Southern Italy 24X 38.36 16.23 ruderal place below street in olive grove
ICE107 Southern Italy 20X 38.38 16.22 old terraced vineyard
ICE111 Southern Italy 21X 40.28 15.65 concrete ramp to field
ICE112 Southern Italy 16X 39.83 16.17 slope in chipping stone place
ICE119 Southern Italy 17X 39.27 16.27 plain place above road embarkment
ICE120 Southern Italy 19X 40.18 16.45 Olive grove on limestone
ICE127 Central Asia 12X 51.34 82.57 NA
ICE130 Central Asia 16X 51.32 82.55 NA
ICE134 Central Asia 21X 51.33 82.19 NA
ICE138 Central Asia 17X 51.65 80.82 NA
ICE150 Central Asia 18X 41.45 70.05 NA
ICE152 Central Asia 12X 41.45 70.05 NA
ICE153 Central Asia 21X 41.45 70.05 NA
ICE163 Southern Tyrol 12X 46.37 11.24 stark
ICE169 Southern Tyrol 19X 46.51 11.33 maessig
ICE173 Southern Tyrol 19X 46.51 11.33 maessig
ICE181 Southern Tyrol 15X 46.36 11.28 ungestoert
ICE21 East Europe 19X 44.34 21.46 fallow field
ICE212 Southern Tyrol 16X 46.34 11.29 maessig
ICE213 Southern Tyrol 19X 46.34 11.29 maessig
ICE216 Southern Tyrol 17X 46.25 11.17 mittel
ICE226 Southern Tyrol 12X 46.63 10.82 gering
ICE228 Southern Tyrol 15X 46.63 10.82 gering
ICE29 East Europe 18X 41.43 23.65 track margin
ICE33 East Europe 16X 41.59 25.20 ruderal
ICE36 East Europe 21X 44.84 20.16 fallow field
ICE49 N-Africa Spain 16X 31.48 -7.45 meadow
ICE50 N-Africa Spain 16X 31.47 -7.42 Juniper-Oak-forest
ICE60 Russia 16X 54.09 60.46 steppe
ICE61 Russia 17X 54.06 60.48 steppe
ICE63 East Europe 17X 46.11 21.95 fallow maize field
ICE7 East Europe 17X 41.43 23.50 grazed meadow
ICE70 Russia 16X 53.04 51.75 Steppe (disturbed)
ICE71 Russia 22X 53.33 49.48 disturbed
ICE72 Russia 20X 53.33 49.48 disturbed
ICE73 Russia 18X 51.31 57.56 steppe
ICE75 Russia 17X 53.09 52.00 Pine forest
ICE79 Southern Tyrol 18X 46.36 11.23 rock outcrops
ICE91 Southern Italy 19X 38.62 16.17 sandy narrow path in olive grove
ICE92 Southern Italy 12X 38.76 16.24 open slope in Quercus ilex forest
ICE93 Southern Italy 17X 39.01 16.47 Road margin
ICE97 Southern Italy 19X 41.62 12.87 olive grove
ICE98 Southern Italy 18X 41.62 12.87 olive grove
Istisu-1 Kaukasus 14X 38.98 48.56 disturbed hillside and roadside
Kastel-1 East Europe 13X 44.64 34.38 open rocky outcrop and adjacent roadside, full sun
Koch-1 East Europe 18X 50.36 29.32 sandy field margin and waste place, full sun
Lag2.2 Kaukasus 14X 41.83 46.28 grazed pasture and rock pile
Leo-1 N-Africa Spain 16X 41.80 -3.11 NA
Lerik1-3 Kaukasus 16X 38.74 48.61 open roadside and trailside
Mer-6 N-Africa Spain 18X 38.92 -6.34 NA
Nemrut-1 Kaukasus 17X 38.64 42.24 NA
Nie1-2 Tuebingen 16X 48.52 8.80 NA
Ped-0 N-Africa Spain 20X 40.74 -3.90 NA
Pra-6 N-Africa Spain 17X 41.05 -3.54 NA
Qui-0 N-Africa Spain 15X 42.69 -6.93 NA
Rue3-1-31 Tuebingen 16X 48.56 9.16 NA
Sha Central Asia 15X 37.29 71.30 NA
Star-8 Tuebingen 13X 48.43 8.82 NA
TueSB30-3 Tuebingen 16X 48.53 9.06 NA
Tuescha9 Tuebingen 14X 48.53 9.05 NA
TueV13 Tuebingen 12X 48.52 9.05 NA
TueWa1-2 Tuebingen 20X 48.53 9.04 NA
Vash-1 Kaukasus 16X 41.24 46.37 shrubby riverbank with Juniperus
Vie-0 N-Africa Spain 18X 42.63 0.76 NA
WalhaesB4 Tuebingen 10X 48.60 9.19 NA
Xan-1 Kaukasus 22X 38.65 48.80 partially shaded roadside and open pasture
Yeg-1 Kaukasus 17X 39.87 45.36 disturbed, open area

Data


Browse all data in our Data Center and see the Readme for more information on released data files and formats.

Tools


Query and select SNPs, indels, structural variants and highly diverged regions for 80 strains with Polymorph, and explore all genomes with GBrowse.

Contact


For any questions concerning the data contact Jun Cao or Korbinian Schneeberger, for any problems downloading/accessing the data contact Joffrey Fitz.