Main Project
GMI-MPI
Download all analyzed data for 1135 strains.Enter Data Center
Subset Projects
WTCHGMott2011 - 19 genomes of Arabidopsis thaliana
The project contains the genomes and transcriptomes of the 19 founders of the MAGIC population of recombinant inbred lines. The website also contains tables of sequence variants and gene models, and the original BAM files.Go to Project Page
SLUHenning2014 - Chi-2 and Seattle-0
Reads and assemblies for Chi-2 and Seattle-0.Enter Data Center
MPICWang2013 - 343 Arabidopsis thaliana accessions
343 strains were sequenced by Monsanto and analyzed by MPI.Enter Data Center Go to Project Page
MPIWang2013 – Bur-0 and C24 Genome templates
While examining effects of transposons on gene expression, we built genome templates of Bur-0 and C24 using the paired-end reads published with MPISchneeberger2011. These reads give about 80x genome coverage and allowed prediction of transposon deletions in Bur-0 and C24 compared to Col-0.Enter Data Center Go to Project Page
CeBiTecRies2012 - Nd-1
Nd-1 was was sequenced by Center for Biotechnology of the University of Bielefeld (CeBiTec) using the Illumina short read platform and the 454 platform.Enter Data Center Go to Project Page
JGIHeazlewood2011 - Arabidopsis thaliana strains sequenced by the DOE Joint Genome Institute
6 strains (Blh-1, Ri-0, Jea, Sakata, Oy-0, and Alc-0) sequenced by the JGI.
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JGIHeazlewood2008 - Bay-0 and Shahdara
The accessions Bay-0 (CS22633) and Shahdara (CS22652) were initially selected for resequencing by the Joint BioEnergy Institute
(JBEI: http://www.jbei.org/) to support cell wall research that had examined cell wall QTLs in Bay-0 x Sha recombinant inbred
line populations (http://www.ncbi.nlm.nih.gov/pubmed/16714406). Sequencing was undertaken by the Joint Genome Institute
(http://www.jgi.doe.gov/) using Illumina short reads.
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GMINordborg2010 - Arabidopsis thaliana strains sequenced by the Gregor Mendel Institute
180 strains sequenced by the GMI.
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Salk - Arabidopsis thaliana strains sequenced by the Salk Institute
171 strains sequenced by the Salk Institute.
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MPISchneeberger2011 - Arabidopsis thaliana assemblies
Here we provide the genome sequences of four Arabidopsis thaliana accessions. The sequences are assembled from Illumina sequence reads only accounting for ~50 to 200x genome coverage. The assembly process followed a homology-guided strategy in order to make use of the Col-0 reference sequence.
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MPICao2010 - 80 Arabidopsis thaliana accessions
As the pilot of 1001 genomes project, we sequenced complete genome of
80 Arabidopsis thaliana accessions selected from 8 regions across
Eurasia with paired end Illumina short reads. We have released the
SNPs and structural variants (SVs) on our FTP site. We have also
deposited the seeds of accessions into ABRC stock center (CS76427).
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MPIcollab2011 - 3 Arabidopsis thaliana accessions
Three additional strains sequenced at MPI by collaborators.
The strains (Ws-2, Tnz-1 and Strand-1) were sequenced by Seth Davis
(Max Planck Institute for Plant Breeding Research, Cologne) and were analyzed at the MPI Tuebingen.
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MPISchneeberger2009 - Est-1 resequenced using genome graphs
Schneeberger, K., Hagmann, J., Ossowski, S., Warthmann, N., Gesing, S., Kohlbacher, O., Weigel, D. Simultaneous alignment of short reads against multiple genomes. Genome Biol. 2009. (Fulltext)
Here we describe the results of the resequencing of Arabidopsis thaliana
Est-1. Est-1 was analyzed in a show case project outlining the advantage
of genome graphs as alignment targets in resequencing projects.
Genome resequencing with short reads generally relies on alignments
against a single reference. GenomeMapper supports simultaneous mapping
of short reads against multiple genomes by integrating related genomes
(e.g., individuals of the same species) into a single graph structure.
It constitutes the first approach for handling multiple references and
introduces representations for alignments against complex structures.
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MPIOssowski2008 - Col-0, Bur-0 and Tsu-1
Ossowski, S., Schneeberger, K., Clark, R. M., Lanz, C., and Weigel, D. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 2008. (Fulltext)
Back in 2007 we wanted to examine the potential of Illumina sequencing
and we produced 15- to 25-fold coverage in Illumina
sequencing-by-synthesis (SBS) reads for the reference accession, Col-0,
and two divergent strains, Bur-0 and Tsu-1. We aligned reads to the
reference genome sequence to assess data quality metrics and to detect
polymorphisms.
Our pipeline for aligning reads and predicting SNPs and indels, SHORE,
is available for download here.
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