What is Arabidopsis thaliana?
Arabidopsis thaliana (commonly known as "Thale cress") is a small flowering weed that grows luxuriantly in the temperate regions of the world. The plant is named after the 16th century botanist Johannes Thal (author of "Sylva Hercynia") who described it for the first time. Arabidopsis is the most favorite model organism for the plant biologists for various reasons. Laibach in mid 90's was the first one to recognize the potential of Arabidopsis as a model organism. It belongs to the Brassicaceae (mustard) family along with economically important crop plants like radish, mustard, cabbage, etc. Currently there are 750+ known natural varieties of Arabidopsis thaliana around the world, which in itself would generate great interest in its evolution and genetics.
Why Arabidopsis ?
Arabidopsis is not an agronomically important plant but its quite useful for studying the molecular and genetic aspects of higher plants.
- The most important aspect about Arabidopsis is that its physiology and development are quite similar to the crop plants and it behaves exactly the same way under experimental conditions. So, whatever that is done in Arabidopsis can be transferred to crop plants quite amenably.
- It has a very small genome (~115mb) that is fully sequenced in 2000 (AGI). Estimated number of genes are around 28,000. The small genome makes it much easier to identify mutations and to evaluate the genomic response to experimental stimuli.
- Arabidopsis is a naturally self pollinating plant and therefore maintaining desired genotype is quite easy, at the same time it is cross compatible also.
- A single plant produces around 6,000 seeds/ generation. This is very critical if one would like to study the inheritance of complex traits and progeny analysis.
- Its life cycle is very short, takes only 6 weeks from germination to mature seed. The size of the plant is very small (~20-30cm) therefore is easy to grow them under controlled laboratory conditions. The short life cycle is a very desirable character for a model plant as it reduces time taken for a given experiment.
- Arabidopsis can be easily transformed with Agrobacterium or any standard chemical mutagens. Most of the molecular and genetic tools are well characterized during the past few years. Transformants can be conveniently screened on a regular MS agar plates with suitable antibiotics.
- Arabidopsis has only 5 chromosomes (2n=10) that makes the meiotic studies a lot more easier.
- Enormous number of mutants and insertion lines and genomic resources are available with stock centers like ABRC and NASC.
Huge research community including academic, government and industry laboratories are around to supplement further.
- The Arabidopsis Information Resource: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
- Genevestigator: Genevestigator is a reference expression database and meta-analysis system. It allows biologists to study the expression and regulation of genes in a broad variety of contexts by summarizing information from hundreds of microarray experiments into easily interpretable results.
- European Arabidopsis Stock Centre: NASC now maintains over 300,000 accessions of Arabidopsis thaliana representing over half a million genotypes
- MIPS Database: MAtDB started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative, but is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities
- NCBI Home page: The NCBI houses genome sequencing data in GenBank and an index of biomedical research articles in PubMed Central and PubMed, as well as other information relevant to biotechnology.
- ExPASy - UniProt Knowledgebase: UniProtKB/Swiss-Prot is a curated protein sequence database which provides a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.)with a minimal level of redundancy and high level of integration with other databases
- Salk Institute Genomic Analysis Laboratory:
- PlantGDB: Resources for plant comparative genomics
- SIGnAL T-DNA Express: Arabidopsis gene mapping tool. Search for T-DNA insertion lines.
- NCBI Nucleotide BLAST: BLASTN programs search nucleotide databases using a nucleotide query.
- TAIR WU-BLAST: Search Arabidopsis genome with nucleotide or protein query. Select the database from menu.
- TAIR SeqViewer: Find out the Physical location of your gene or a sequence of interest on the Arabidopsis genome.
- EBI tools-ClustalW2: Do multiple alignment of your amino acid and DNA sequence here
- Genscan: Identification of complete gene structures in genomic DNA.
- Plant Genome Data Base: Look for the homolog of your gene of interest in sequenced plant genomes.