Why arabidopsis thaliana

Synanthropy: Occurrence of an organism in association with human settlement, where human activities directly or indirectly generate favorable environmental conditions for the organism. Ultramafic soils: Infertile, nutrient poor soils derived from so-called serpentine minerals, which are common in zones of tectonic activity. The popularity of A. The ease and speed with which experiments can be conducted on A.

The many uses of Arabidopsis as the universal reference plant continue to expand, particularly in the field of systems biology Brady et al. Many of the traits that render A. Indeed, the natural history of A. Within these six evolutionary lineages, a number of phylogenetically as yet unresolved taxa have been described, as have auto- and allopolyploidization events see Glossary. The divergence time of the common ancestor of these species and the A. Thus, divergence occurred immediately before or during the transition from a warm period to progressively colder climates, followed by rapid glacial cycles from 3 Mya until the latest glacial maximum about 18, years ago.

There has even been a natural allopolyploidization event between A. From left to right: A. The individuals shown here do not reflect the large within-species morphological diversity, particularly in leaf shape, among different accessions of A.

Work in recent years has increasingly emphasized the relevance of conducting experiments on A. This important development will benefit from a more detailed knowledge of the unique and shared features of its natural and evolutionary history, as well as of the natural environments that host populations of A.

Arabidopsis thaliana is recognized as native to Western Eurasia Figure 3. The species is a colonizer and pioneer plant of disturbed, poor, stony or shallow soils, and it can also be found in nutrient-poor, often sandy, meadow and forest habitats Mitchell-Olds and Schmitt, Similarly, the species closely related to A. Sequence polymorphism data provide evidence for a historical expansion of the A. It has been suggested that A.

There is also clear evidence for additional glacial refugia for A. This reflects an evolutionary history of vast climatic and environmental fluctuations, likely including a series of alternating phases of population size contraction and expansion with migration and admixture following glacial cycles Beck et al. In the past few years, A. The present climatic and geographic range of A. Areas colored in red correspond to the continuous distribution of A.

This map is based on a partial map kindly provided by Matthias Hoffmann personal communication, November , with manual additions to the southern hemisphere Bresinsky et al.

In addition to—and likely permitting—the rapid expansion of its range, A. Estimates place these transitions as having occurred, based on different approaches, at around 0. By contrast, most species closely related to A. In addition to selfing, A. Vegetative A.

The leaves of A. These morphological differences are likely to constitute adaptations to differing environments. By comparison to its sister group of species, the flowering of A. Seeds of A. These features of A. The complexity of organ architecture appears to be reduced in A. Notably, its roots mostly contain only a single layer of each specialized cell type, a feature that is optimal for in vivo imaging Figure 4 De Lucas and Brady, This organization differs from the roots of its close relative A.

The metabolic cost of building an A. Longitudinal left and transverse right confocal sections of A. TAIR collects and makes available the information arising from these efforts. View of Arabidopsis thaliana [Back to top] History of Arabidopsis thaliana as a research organism. The earliest report of a mutant that I know of was in by A. Laibach first summarized the potential of Arabidopsis thaliana as a model organism for genetics in - he did some work on it much earlier though, publishing its correct chromosome number in The first collection of induced mutants was made by Laibach's student E.

Her thesis was submitted in , the work published in Veleminsky in Czechoslovakia and G. He wrote a more easily found one in Ann. Both go through some of the early history of the use of Arabidopsis in the laboratory, though the longer one has all the details.

In Methods in Arabidopsis Research , eds C. These accessions are quite variable in terms of form and development e. Advantages of using Saccharomyces Cerevisiae as a Model Organism.

As one of the simplest eukaryotes containing membrane bound organelles , and i Advantages of using Escherichia Coli as a Model Organism. Courtesy of Christoph S Advantages of using Caenorhabditis Elegans as a Model Organism. No Related Papers. You have successfully logged out. Open in a new tab. Privacy Disclaimer Sitemap. Lessons from the sequencing of the genome of a unicellular cyanobacterium, Synechocystis SP. Plant Physiol. Plant Mol. Apweiler, R. Collaborative Computer Project 11 Newsletter no.

Bent, A. RPS2 of Arabidopsis thaliana a leucine-rich repeat class of plant disease resistance genes. Skowyra, D. F box proteins are receptors that recruit phsphorylated substrates to the SCF ubiquitin-ligase complex. Cell 91 , — Joazeiro, C. RING finger proteins: mediators of ubiquitin ligase activity. Cell , — Rubin, G.

Comparative genomics of the eukaryotes. Delcher, A. Alignment of whole genomes. Blanc, G. Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12 , — Wendel, J. Genome evolution in polyploids. Gaut, B. DNA sequence evidence for the segmental allotetraploid origin of maize.

USA 94 , — Ku, H. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. USA 97 , — Noel, L. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11 , — Ellis, J.

Structure, function, and evolution of plant disease resistance genes. Trends Plant Sci. Tanksley, S. High density molecular linkage maps of the tomato and potato genomes. Genetics , — Moore, G. Grasses, line up and form a circle. Acarkan, A. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Cavell, A. A 30 centimorgan segment of Arabidopsis thaliana chromosome 4 has six collinear homologues within the Brassica napus genome.

Genome 41 , 62—69 O'Neill, C. Comparative physical mapping of segments of the genome of Brassica oleracea var alboglabra that are homologous to sequenced regions of the chromosomes 4 and 5 of Arabidopsis thaliana.

Wolfe, K. Date of the monocot-dicot divergence estimated from the chloroplast DNA sequence data. USA 86 , — Identification and analysis of homologous segments of the genomes of rice and Arabidopsis thaliana.

Genome 42 , — Sequence level analysis of homologous segments of the genomes of rice and Arabidopsis thaliana. Genome Res. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Research 6 , — Unseld, M. The mitochondrial genome in Arabidopsis thaliana contains 57 genes in , nucleotides. Palmer, J. Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Le, Q.

Transposon diversity in Arabidopsis thaliana. Yu, Z. Genetics in the press. Feschotte, C. Evidence that a family of miniature inverted-repeat transposable elements MITEs from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon.

Martienssen, R. Transposons, DNA methylation and gene control. Trends Genet. Singer, T. Genes Dev. SanMiguel, P.

Nested retrotransposons in the intergenic regions of the maize genome. Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana , suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Fransz, P. Cytogenetics for the model system Arabidopsis thaliana. Richards, E. Isolation of a higher eukarotic telomere from Arabidopsis thaliana. Cell 53 , — Round, E. Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.

The complete sequence of a heterochromatic island from a higher eukaryote. Integrated cytogenetic map of chromosome arm 4S of A. Paulsen, I. Jr Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes. Jr Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae.

FEBS Lett. Hirsch, R. D, Spalding, E. A role for the AKT1 potassium channel in plant nutrition. Slayman, C. Depolarization of the plasma membrane of Neurospora during active transport of glucose: evidence for a proton-dependent cotransport system.

USA 71 , — Ryan, C. Systemin: a polypeptide signal for plant defensive genes. Eisen, J. A phylogenomic study of DNA repair genes, proteins, and processes. Selby, C. Structure and function of transcription-repair coupling factor.

Structural domains and binding properties. Britt, A. Molecular genetics of DNA repair in higher plants. Dangl, M. Response to Aravind, L. Second Family of Histone Deacetylases. Science , Cao, X. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.

Henikoff, S. A DNA methyltransferase homologue with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Hung, M. Drosophila proteins related to vertebrate DNA 5-cytosine methyltransferases.

Proc Natl Acad. Dalmay, T. An RNA-dependent-RNA polymerase in Arabidopsis is required for post transcriptional gene silencing mediated by a transgene but not by a virus—the truth. Riechmann, J. A genomic perspective on plant transcription factors. Plant Biol. Liljegren, S. Pelaz, S. Canaday, J. Higher plant cells: gamma-tubulin and microtubule nucleation in the absence of centrosomes.

Bassham, D. Unique features of the plant vacuolar sorting machinery. Cell Biol. Zheng, Z. The Rrop GTPase switch turns on polar growth in pollen.

Triggering the cell cycle in plants. Trends Cell Biol. Heese, M. Cytokinesis in flowering plants: cellular process and developmental integration. Plants, animals, and the logic of development. Wang, D. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. B Bio. Torii, K. Receptor kinase activation and signal transduction in plants: an emerging picture. Yeh, K. USA 95 , — McCarty, D. Conservation and innovation in plant signaling pathways.

Weiss, C. USA 91 , — Bowler, C. Cyclic GMP and calcium mediate phytochrome phototransduction. Cell 77 , 73—81 Stepanova, A. Ethylene signaling: from mutants to molecules. Urao, T. Two-component systems in plant signal transduction. Makino, S. Genes encoding pseudo-response regulators: Insight into His-to-Asp phosphorelay and circadian rhythm in Arabidopsis thaliana.

Plant Cell Physiol. D'Agostino, I. Phosphorelay signal transduction: the emerging family of plant response regulators. Trends Biol. Strayer, C. Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homologue. Stahl, E. Plant-Pathogen arms races at the molecular level. McDowell, J. Signal transduction in the plant innate immune response.

Trends Biochem. Van der Biezen, E. Plant disease-resistance proteins and the gene-for-gene concept. Trends Biochem Sci. Belvin, M. A conserved signaling pathway: the Drosophila toll-dorsal pathway. Uren, A. Identification of paracaspases and metacaspases: Two ancient families of caspase-like proteins, one of which plays a key role in MALT lymphoma.

Cell 6 , — Fankhauser, C. Light control of plant development. Briggs, W. Blue-light photoreceptors in higher plants. Christie, J. LOV light, oxygen, or voltage domains of the blue-light photoreceptor phototropin nph1 : binding sites for the chromophore flavin mononucleotide. Golbeck, J. Structure and function of photosystem I. Maier, R. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing.

Buchanan, B. Mekhedov, S. Toward a functional catalog of the plant genome. A survey of genes for lipid biosynthesis. Somerville, C. Photorespiration deficient mutants of Arabidopsis thaliana lacking mitochrondrial serine transhydroxymethylase activity. Richmond, T. The cellulose synthase superfamily. Plant Physiol , — Carpita, N. Vergara C: A recipe for cellulose. De Vries, H. Sur la loi de disjonction des hybrides. Paris , — Alonso-Blanco, C. Naturally occurring variation in Arabidopsis : an underexploited resource for plant genetics.

Chory, J. Functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiology , — Burge, C. Prediction of complete gene structures in human genomic DNA.

Lukashin, A. Uberbacher, E. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. USA 88 , — Salzberg, S. Interpolated Markov models for eukaryotic gene finding. Genomics 59 , 24 —31 Hebsgaard, S. Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information. Brendel, V. Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA.

Quackenbush, J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Huang, X. A tool for analyzing and annotating genomic sequences. Genomics 46 , 37—45 Altschul, S. Basic local alignment search tool. Morgenstern, B. Murzin, A.