Projects Overview
JGIHeazlewood2011 - Arabidopsis thaliana strains sequenced by the DOE Joint Genome Institute
6 strains 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. Go to project page >>
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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. Go to project page (external site) >>
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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. Go to project page >>
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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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