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:
- Spain and North Africa
- Swabia, in the southwest of Germany
- South Tyrol, in the North of Italy
- Southern Italy
- Eastern Europe
- Caucasus
- Southern Russia and
- Central Asia.
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 / Ey1.5 | 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 / Bolin-1 | East Europe | 15X | 44.46 | 25.74 | fallow field |
| ICE102 / Galdo-1 | Southern Italy | 18X | 40.57 | 15.32 | field margin close to shrub |
| ICE104 / Lago-1 | Southern Italy | 22X | 39.18 | 16.26 | meadow |
| ICE106 / Mammo-1 | Southern Italy | 24X | 38.36 | 16.23 | ruderal place below street in olive grove |
| ICE107 / Mammo-2 | Southern Italy | 20X | 38.38 | 16.22 | old terraced vineyard |
| ICE111 / Monte-1 | Southern Italy | 21X | 40.28 | 15.65 | concrete ramp to field |
| ICE112 / Moran-1 | Southern Italy | 16X | 39.83 | 16.17 | slope in chipping stone place |
| ICE119 / Timpo-1 | Southern Italy | 17X | 39.27 | 16.27 | plain place above road embarkment |
| ICE120 / Valsi-1 | Southern Italy | 19X | 40.18 | 16.45 | Olive grove on limestone |
| ICE127 / Kly-1 | Central Asia | 12X | 51.34 | 82.57 | NA |
| ICE130 / Kly-4 | Central Asia | 16X | 51.32 | 82.55 | NA |
| ICE134 / Koz-2 | Central Asia | 21X | 51.33 | 82.19 | NA |
| ICE138 / Leb-3 | Central Asia | 17X | 51.65 | 80.82 | NA |
| ICE150 / Sij-1 | Central Asia | 18X | 41.45 | 70.05 | NA |
| ICE152 / Sij-2 | Central Asia | 12X | 41.45 | 70.05 | NA |
| ICE153 / Sij-4 | Central Asia | 21X | 41.45 | 70.05 | NA |
| ICE163 / Altenb-2 | Southern Tyrol | 12X | 46.37 | 11.24 | stark |
| ICE169 / Bozen-1.1 | Southern Tyrol | 19X | 46.51 | 11.33 | maessig |
| ICE173 / Bozen-1.2 | Southern Tyrol | 19X | 46.51 | 11.33 | maessig |
| ICE181 / Mitterberg-1-181 | Southern Tyrol | 15X | 46.36 | 11.28 | ungestoert |
| ICE21 / Petro-1 | East Europe | 19X | 44.34 | 21.46 | fallow field |
| ICE212 / Castelfed-4.1 | Southern Tyrol | 16X | 46.34 | 11.29 | maessig |
| ICE213 / Castelfed-4-213 | Southern Tyrol | 19X | 46.34 | 11.29 | maessig |
| ICE216 / Rovero-1 | Southern Tyrol | 17X | 46.25 | 11.17 | mittel |
| ICE226 / Vezzano-2.1 | Southern Tyrol | 12X | 46.63 | 10.82 | gering |
| ICE228 / Vezzano-2.2 | Southern Tyrol | 15X | 46.63 | 10.82 | gering |
| ICE29 / Slavi-1 | East Europe | 18X | 41.43 | 23.65 | track margin |
| ICE33 / Jablo-1 | East Europe | 16X | 41.59 | 25.20 | ruderal |
| ICE36 / Dobra-1 | East Europe | 21X | 44.84 | 20.16 | fallow field |
| ICE49 / Aitba-2 | N-Africa Spain | 16X | 31.48 | -7.45 | meadow |
| ICE50 / Toufl-1 | N-Africa Spain | 16X | 31.47 | -7.42 | Juniper-Oak-forest |
| ICE60 / Stepn-2 | Russia | 16X | 54.09 | 60.46 | steppe |
| ICE61 / Stepn-1 | Russia | 17X | 54.06 | 60.48 | steppe |
| ICE63 / Copac-1 | East Europe | 17X | 46.11 | 21.95 | fallow maize field |
| ICE7 / Lecho-1 | East Europe | 17X | 41.43 | 23.50 | grazed meadow |
| ICE70 / Borsk-2 | Russia | 16X | 53.04 | 51.75 | Steppe (disturbed) |
| ICE71 / Shigu-1 | Russia | 22X | 53.33 | 49.48 | disturbed |
| ICE72 / Shigu-2 | Russia | 20X | 53.33 | 49.48 | disturbed |
| ICE73 / Kidr-1 | Russia | 18X | 51.31 | 57.56 | steppe |
| ICE75 / Krazo-2 | Russia | 17X | 53.09 | 52.00 | Pine forest |
| ICE79 / Voeran-1 | Southern Tyrol | 18X | 46.36 | 11.23 | rock outcrops |
| ICE91 / Angel-1 | Southern Italy | 19X | 38.62 | 16.17 | sandy narrow path in olive grove |
| ICE92 / Angit-1 | Southern Italy | 12X | 38.76 | 16.24 | open slope in Quercus ilex forest |
| ICE93 / Apost-1 | Southern Italy | 17X | 39.01 | 16.47 | Road margin |
| ICE97 / Ciste-1 | Southern Italy | 19X | 41.62 | 12.87 | olive grove |
| ICE98 / Ciste-2 | 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 / 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 / Ara-1 | 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 / Tu-Scha-9 | Tuebingen | 14X | 48.53 | 9.05 | NA |
| TueV13 / TueV-13 | 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.