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About Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. Arabidopsis is a member of the mustard (Brassicaceae) family, which includes cultivated species such as cabbage and radish. Arabidopsis is not of major agronomic significance, but it offers important advantages for basic research in genetics and molecular biology. Arabidopsis thaliana has a genome size of approx. 135 Mbase, and a haploid chromosome number of 5. (From TAIR).
Genome Sequencing and Gene Prediction (Release TAIR10)
The complete genome sequence of Arabidiopsis thaliana was first published by the Arabidopsis Genome Initiative in 2000 [1] and was determined by a BAC-by-BAC sequencing strategy anchored to chromosomes using a variety of genetic and physical maps. Gene annotations use cDNA and EST data as well as manual updates informed by cross-species alignments, peptides and community input regarding missing and incorrectly annotated genes. The assembly and annotation are subject to ongoing updates. This browser is based on data from version 10 of The Arabidopsis Information Resource (TAIR) database, released in November 2010. [more].
Data Usage
The 1001 Arabidopsis Genomes project has released data in a pre-publication format from the Salk Institute, WTCHG, MPI, and GMI. This is provided freely to be used by anyone, but the 1001 Arabidopsis Genomes consortium have requested that the scientific ethics of other groups publishing on this pre-publication data are respected. This is outlined in detail in the Fort Lauderdale agreement; in brief, small scale analysis, eg, the analysis of a single locus is an expected use of the data which can be published on without any expectation of coordination. In contrast, large scale, genomewide analysis is expected to be either coordinated with the 1001 Arabidopsis Genomes consortium in some manner or published after initial papers. More details on the reasoning for this and details are given in the Fort Lauderdale document.
Gramene/Ensembl Genomes Annotation
Additional annotations generated by the Gramene/Ensembl Genomes projects include:
- The standard set of Gramene analyses detailed here.
- Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.
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The Arabidopsis variation database contains data from the screening of 1179 strains by Nordborg et al. using the Affymetrix 250k Arabidopsis SNP chip, and an updated data set produced
through a
collaboration between Richard Mott at the
Wellcome Trust Centre for
Human Genetics in Oxford, Paula Kover at the University of Bath, and EBI,
funded by the BBSRC which involved the resequencing of 18 Arabidopsis lines. It also contains 392 strains from the 1001 Genomes Project.
- 80 strains from the Cao pilot study
- 132 strains from a study by the Salk Institute
- 180 strains from a study by the Nordborg group at GMI
- Mappings for probes from the following arrays were also added to the functional genomics schema:
Links
References
- Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796-815. PubMed ID: 11130711
- Swarbreck D, Wilks C, Lamesch P, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2008;36(Database issue):D1009-1014. PubMed ID: 17986450
- Richard M. Clark, et al. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science 317, 338 (2007); PubMed ID: 17641193; DOI: 10.1126/science.1138632
- S. Atwell et al., Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Mar 24 (epub); PubMed ID: 20336072; DOI: 10.1038/nature08800
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