Download all analyzed data for 1135 strains (VCFs, SNP matrix, pseudogenomes).
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.
Reads and assemblies for Chi-2 and Seattle-0.
343 strains were sequenced by Monsanto and analyzed by MPI.
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.
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.
6 strains (Blh-1, Ri-0, Jea, Sakata, Oy-0, and Alc-0) sequenced by the JGI.
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.
180 strains sequenced by the GMI.
171 strains sequenced by the Salk Institute.
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.
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).
Three additional accessions 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.
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.
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.