Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally considered a weed.
A winter annual with a relatively short lifecycle, A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a relatively small genome of around 135 megabase pairs. It was the first plant to have its genome sequenced, and is an important tool for understanding the molecular biology of many plant traits, including flower development and light sensing.
Description
Arabidopsis thaliana is an annual (rarely biennial) plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, with a few leaves also on the flowering stem. The basal leaves are green to slightly purplish in color, 1.5–5 cm long, and 2–10 mm broad, with an entire to coarsely serrated margin; the stem leaves are smaller and unstalked, usually with an entire margin. Leaves are covered with small, unicellular hairs called trichomes. The flowers are 3 mm in diameter, arranged in a corymb; their structure is that of the typical Brassicaceae. The fruit is a silique 5–20 mm long, containing 20–30 seeds.Flora of NW Europe: Arabidopsis thaliana Blamey, M. & Grey-Wilson, C. (1989). Flora of Britain and Northern Europe. Flora of Pakistan: Arabidopsis thaliana Flora of China: Arabidopsis thaliana Roots are simple in structure, with a single primary root that grows vertically downward, later producing smaller lateral roots. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium.
A. thaliana can complete its entire lifecycle in six weeks. The central stem that produces flowers grows after about 3 weeks, and the flowers naturally self-pollinate. In the lab, A. thaliana may be grown in Petri plates, pots, or hydroponics, under fluorescent lights or in a greenhouse.
Taxonomy The plant was first described in 1577 in the Harz Mountains by (1542–1583), a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1753, Carl Linnaeus renamed the plant Arabis thaliana in honor of Thal. In 1842, German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The generic name, Arabidopsis, comes from Greek, meaning "resembling Arabis" (the genus in which Linnaeus had initially placed it).
Thousands of natural inbred accessions of A. thaliana have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation, which can be used to study the adaptation of this species to different environments.
Distribution and habitat
A. thaliana is native to Europe, Asia, and Africa, and its geographic distribution is rather continuous from the Mediterranean to Scandinavia and Spain to Greece. It also appears to be native in tropical alpine ecosystems in Africa and perhaps South Africa. It has been introduced and naturalized worldwide, including in North America around the 17th century.
A. thaliana readily grows and often pioneers rocky, sandy, and calcareous soils. It is generally considered a weed, due to its widespread distribution in agricultural fields, roadsides, railway lines, waste ground, and other disturbed habitats, but due to its limited competitive ability and small size, it is not categorized as a noxious weed. Like most Brassicaceae species, A. thaliana is edible by humans in a salad or cooked, but its use as a spring vegetable is not widespread.
Use as a model organism
Botanists and biologists began to research A. thaliana in the early 1900s, and the first systematic description of mutants was done around 1945. TAIR: About Arabidopsis A. thaliana is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development. Although A. thaliana the plant has little direct significance for agriculture, A. thaliana the model organism has revolutionized our understanding of the genetic, cellular, and molecular biology of flowering plants.
The first mutant in A. thaliana was documented in 1873 by Alexander Braun, describing a double flower phenotype (the mutated gene was likely Agamous, cloned and characterized in 1990). Friedrich Laibach (who had published the chromosome number in 1907) did not propose A. thaliana as a model organism, though, until 1943. His student, Erna Reinholz, published her thesis on A. thaliana in 1945, describing the first collection of A. thaliana mutants that they generated using X-ray mutagenesis. Laibach continued his important contributions to A. thaliana research by collecting a large number of accessions (often questionably referred to as "ecotypes"). With the help of Albert Kranz, these were organised into a large collection of 750 natural accessions of A. thaliana from around the world.
In the 1950s and 1960s, John Langridge and George Rédei played an important role in establishing A. thaliana as a useful organism for biological laboratory experiments. Rédei wrote several scholarly reviews instrumental in introducing the model to the scientific community. The start of the A. thaliana research community dates to a newsletter called Arabidopsis Information Service, established in 1964. The first International Arabidopsis Conference was held in 1965, in Göttingen, Germany.
In the 1980s, A. thaliana started to become widely used in plant research laboratories around the world. It was one of several candidates that included maize, petunia, and tobacco. The latter two were attractive, since they were easily transformable with the then-current technologies, while maize was a well-established genetic model for plant biology. The breakthrough year for A. thaliana as a model plant was 1986, in which T-DNA-mediated transformation and the first cloned A. thaliana gene were described.
Genomics
Nuclear genome
Due to the small size of its genome, and because it is diploid, Arabidopsis thaliana is useful for genetic mapping and sequencing — with about 157 megabase pairs and five chromosomes, A. thaliana has one of the smallest genomes among plants. It was long thought to have the smallest genome of all flowering plants,(Leutwileret al., 1984). In our survey Arabidopsis ... but that title is now considered to belong to plants in the genus Genlisea, order Lamiales, with Genlisea tuberosa, a carnivorous plant, showing a genome size of approximately 61 Mbp. It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative. The most up-to-date version of the A. thaliana genome is maintained by The Arabidopsis Information Resource (TAIR).
The genome encodes ~27,600 protein-coding genes and about 6,500 non-coding genes. However, the Uniprot database lists 39,342 proteins in their Arabidopsis reference proteome. Among the 27,600 protein-coding genes 25,402 (91.8%) are now annotated with "meaningful" product names, although a large fraction of these proteins is likely only poorly understood and only known in general terms (e.g. as "DNA-binding protein without known specificity"). Uniprot lists more than 3,000 proteins as "uncharacterized" as part of the reference proteome.
Chloroplast genome
The plastome of A. thaliana is a 154,478 base-pair-long DNA molecule, a size typically encountered in most flowering plants (see the list of sequenced plastomes). It comprises 136 genes coding for small subunit ribosomal proteins (rps, in yellow: see figure), large subunit ribosomal proteins (rpl, orange), hypothetical chloroplast open reading frame proteins (ycf, lemon), proteins involved in photosynthetic reactions (green) or in other functions (red), ribosomal RNAs (rrn, blue), and transfer RNAs (trn, black).
Mitochondrial genome
The mitochondrial genome of A. thaliana is 367,808 base pairs long and contains 57 genes. There are many repeated regions in the A. thaliana mitochondrial genome. The largest repeats recombine regularly and isomerize the genome. Like most plant mitochondrial genomes, the A. thaliana mitochondrial genome exists as a complex arrangement of overlapping branched and linear molecules in vivo.
Genetics
Genetic transformation of A. thaliana is routine, using Agrobacterium tumefaciens to transfer DNA into the plant genome. The current protocol, termed "floral dip", involves simply dipping floral buds into a solution containing Agrobacterium carrying a plasmid of interest and a detergent. This method avoids the need for tissue culture or plant regeneration.
The A. thaliana gene knockout collections are a unique resource for plant biology made possible by the availability of high-throughput transformation and funding for genomics resources. The site of T-DNA insertions has been determined for over 300,000 independent transgenic lines, with the information and seeds accessible through online T-DNA databases. Through these collections, insertional mutants are available for most genes in A. thaliana.
Characterized accessions and mutant lines of A. thaliana serve as experimental material in laboratory studies. The most commonly used background lines are Ler (Landsberg erecta), and Col, or Columbia. Other background lines less-often cited in the scientific literature are Ws, or Wassilewskija, C24, Cvi, or Cape Verde Islands, Nossen, etc. (see for ex.) Sets of closely related accessions named Col-0, Col-1, etc., have been obtained and characterized; in general, mutant lines are available through stock centers, of which best-known are the Nottingham Arabidopsis Stock Center-NASC and the Arabidopsis Biological Resource Center-ABRC in Ohio, USA. The Col-0 accession was selected by Rédei from within a (nonirradiated) population of seeds designated 'Landsberg' which he received from Laibach. Columbia (named for the location of Rédei's former institution, University of Missouri-Columbia) was the reference accession sequenced in the Arabidopsis Genome Initiative. The Later (Landsberg erecta) line was selected by Rédei (because of its short stature) from a Landsberg population he had mutagenized with X-rays. As the Ler collection of mutants is derived from this initial line, Ler-0 does not correspond to the Landsberg accessions, which designated La-0, La-1, etc.
Trichome formation is initiated by the GLABROUS1 protein. Knockouts of the corresponding gene lead to glabrous plants. This phenotype has already been used in gene editing experiments and might be of interest as visual marker for plant research to improve gene editing methods such as CRISPR/Cas9.
Non-Mendelian inheritance controversy In 2005, scientists at Purdue University proposed that A. thaliana possessed an alternative to previously known mechanisms of DNA repair, producing an unusual pattern of inheritance, but the phenomenon observed (reversion of mutant copies of the HOTHEAD gene to a wild-type state) was later suggested to be an artifact because the mutants show increased outcrossing due to organ fusion.Washington Post summary.
Lifecycle
The plant's small size and rapid lifecycle are also advantageous for research. Having specialized as a spring ephemeral, it has been used to found several laboratory strains that take about 6 weeks from germination to mature seed. The small size of the plant is convenient for cultivation in a small space, and it produces many seeds. Further, the selfing nature of this plant assists genetic experiments. Also, as an individual plant can produce several thousand seeds, each of the above criteria leads to A. thaliana being valued as a genetic model organism.
Cellular biology