Arabidopsis thaliana
Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. "A. thaliana" is considered a weed; it is found along the shoulders of roads and in disturbed land. 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 around 135 megabase pairs. It was the first plant to have its genome sequenced, and is a popular 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 siliqua 5–20 mm long, containing 20–30 seeds. 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 it does not enjoy widespread use as a spring vegetable. 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. "A. thaliana" is now widely used for studying plant sciences, including genetics, evolution, population genetics, and plant development. Although "A. thaliana" has little direct significance  for agriculture, several of its traits make it a useful model for understanding 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, 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. 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 "Arabidopsis" mitochondrial genome. The largest repeats recombine regularly and isomerize the genome. Like most plant mitochondrial genomes, the "Arabidopsis" 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 flowers 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 L"er" (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 L"er" collection of mutants is derived from this initial line, L"er"-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. 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. "Arabidopsis" is often the model for study of SNAREs in plants. This has shown SNAREs to be heavily involved in vesicle trafficking. Zheng et al. 1999 found an "Arabidopsis" SNARE called is probably essential to Golgi-vacuole trafficking. This is still a wide open field and plant  SNAREs' role in trafficking remains understudied. DNA repair. The DNA of plants is vulnerable to ultraviolet light, and DNA repair mechanisms have evolved to avoid or repair genome damage caused by UV. Kaiser et al. showed that in "A. thaliana" cyclobutane pyrimidine dimers (CPDs) induced by UV light can be repaired by expression of CPD photolyase. Development. Flower development. "A. thaliana "has been extensively studied as a model for flower development. The developing flower has four basic organs - sepals, petals, stamens, and carpels (which go on to form pistils). These organs are arranged in a series of whorls, four sepals  on the outer whorl, followed by four petals inside this, six stamens, and a central carpel region. Homeotic mutations in "A. thaliana" result in the change of one organ to another—in the case of the "agamous" mutation, for example, stamens become petals and carpels are replaced with a new flower, resulting in a recursively repeated sepal-petal-petal pattern. Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz. According to this model, floral organ identity genes are divided into three classes - class A genes (which affect sepals  and petals), class B genes (which affect petals and stamens), and class C genes (which affect stamens and carpels). These genes code for transcription factors that combine to cause tissue specification in their respective regions during development. Although developed through study of "A. thaliana" flowers, this model is generally applicable to other flowering plants. Leaf development. Studies of "A. thaliana" have provided considerable insights with regards to the genetics of leaf morphogenesis, particularly in dicotyledon-type plants. Much of the understanding has come from analyzing mutants in leaf development, some of which were identified in the 1960s, but were not  analysed with genetic and molecular techniques until the mid-1990s. "A. thaliana" leaves are well suited to studies of leaf development because they are relatively simple and stable. Using "A. thaliana", the genetics behind leaf shape development have become more clear and have been broken down into three stages: The initiation of the leaf primordium, the establishment of dorsiventrality, and the development of a marginal meristem. Leaf primordia are initiated by the suppression of the genes and proteins of class I "KNOX" family (such as "SHOOT APICAL MERISTEMLESS"). These class I KNOX proteins directly suppress gibberellin biosynthesis in the leaf primordium . Many genetic factors were found to be involved in the suppression of these class I "KNOX" genes in leaf primordia (such as "ASYMMETRIC LEAVES1," "BLADE-ON-PETIOLE1", "SAWTOOTH1", etc.). Thus, with this suppression, the levels of gibberellin increase and leaf primordium initiate growth. The establishment of leaf dorsiventrality is important since the dorsal (adaxial) surface of the leaf is different from the ventral (abaxial) surface. Microscopy. "A. thaliana" is well suited for light microscopy analysis. Young seedlings on the whole, and their roots in particular, are relatively translucent. This, together with their small size, facilitates live cell imaging using both  fluorescence and confocal laser scanning microscopy. By wet-mounting seedlings in water or in culture media, plants may be imaged uninvasively, obviating the need for fixation and sectioning and allowing time-lapse measurements. Fluorescent protein constructs can be introduced through transformation. The developmental stage of each cell can be inferred from its location in the plant or by using fluorescent protein markers, allowing detailed developmental analysis. Physiology. Light sensing, light emission, and circadian biology. The photoreceptors phytochromes A, B, C, D, and E mediate red light-based phototropic response. Understanding the function of these receptors has helped plant biologists understand  the signaling cascades that regulate photoperiodism, germination, de-etiolation, and shade avoidance in plants. The genes "FCA", "fy", "fpa", "LUMINIDEPENDENS" ("ld"), "fly", "fve" and "FLOWERING LOCUS C" ("FLC") are involved in photoperiod triggering of flowering and vernalization. Specifically Lee et al 1994 find "ld" produces a homeodomain and Blazquez et al 2001 that "fve" produces a WD40 repeat. The UVR8 protein detects UV-B light and mediates the response to this DNA-damaging wavelength. "A. thaliana" was used extensively in the study of the genetic basis of phototropism, chloroplast alignment, and stomal aperture and other blue light-influenced processes. These  traits respond to blue light, which is perceived by the phototropin light receptors. "Arabidopsis" has also been important in understanding the functions of another blue light receptor, cryptochrome, which is especially important for light entrainment to control the plants' circadian rhythms. When the onset of darkness is unusually early, "A. thaliana" reduces its metabolism of starch by an amount that effectively requires division. Light responses were even found in roots, previously thought to be largely insensitive to light. While the gravitropic response of "A. thaliana" root organs is their predominant tropic response, specimens treated with mutagens and selected for the  absence of gravitropic action showed negative phototropic response to blue or white light, and positive response to red light, indicating that the roots also show positive phototropism. In 2000, Dr. Janet Braam of Rice University genetically engineered "A. thaliana" to glow in the dark when touched. The effect was visible to ultrasensitive cameras. Multiple efforts, including the Glowing Plant project, have sought to use "A. thaliana" to increase plant luminescence intensity towards commercially viable levels. On the Moon. On January 2, 2019, China's Chang'e-4 lander brought "A. thaliana" to the moon. A small microcosm 'tin' in the lander contained  A. thaliana, seeds of potatoes, and silkworm eggs. As plants would support the silkworms with oxygen, and the silkworms would in turn provide the plants with necessary carbon dioxide and nutrients through their waste, researchers will evaluate whether plants successfully perform photosynthesis, and grow and bloom in the lunar environment. Plant–pathogen interactions. Understanding how plants achieve resistance is important to protect the world's food production, and the agriculture industry. Many model systems have been developed to better understand interactions between plants and bacterial, fungal, oomycete, viral, and nematode pathogens. "A. thaliana" has been a powerful tool for the  study of the subdiscipline of plant pathology, that is, the interaction between plants and disease-causing pathogens. The use of "A. thaliana" has led to many breakthroughs in the advancement of knowledge of how plants manifest plant disease resistance. The reason most plants are resistant to most pathogens is through nonhost resistance - not all pathogens will infect all plants. An example where "A. thaliana" was used to determine the genes responsible for nonhost resistance is "Blumeria graminis", the causal agent of powdery mildew of grasses. "A. thaliana" mutants were developed using the mutagen ethyl methanesulfonate and screened to identify mutants  with increased infection by "B. graminis". The mutants with higher infection rates are referred to as" PEN "mutants due to the ability of "B. graminis" to penetrate "A. thaliana" to begin the disease process. The "PEN" genes were later mapped to identify the genes responsible for nonhost resistance to "B. graminis". In general, when a plant is exposed to a pathogen, or nonpathogenic microbe, an initial response, known as PAMP-triggered immunity (PTI), occurs because the plant detects conserved motifs known as pathogen-associated molecular patterns (PAMPs). These PAMPs are detected by specialized receptors in the host known as pattern  recognition receptors (PRRs) on the plant cell surface. The best-characterized PRR in "A. thaliana" is FLS2 (Flagellin-Sensing2), which recognizes bacterial flagellin, a specialized organelle used by microorganisms for the purpose of motility, as well as the ligand flg22, which comprises the 22 amino acids recognized by FLS2. Discovery of FLS2 was facilitated by the identification of an "A. thaliana" ecotype, Ws-0, that was unable to detect flg22, leading to the identification of the gene encoding FLS2. . Both flagellin and UV-C act similarly to increase homologous recombination in "A. thaliana", as demonstrated by Molinier et al. 2006. Beyond  this somatic effect, they found this to extend to subsequent generations of the plant. A second PRR, EF-Tu receptor (EFR), identified in "A. thaliana", recognizes the bacterial EF-Tu protein, the prokaryotic elongation factor used in protein synthesis, as well as the laboratory-used ligand elf18. Using "Agrobacterium"-mediated transformation, a technique that takes advantage of the natural process by which "Agrobacterium" transfers genes into host plants, the EFR gene was transformed into "Nicotiana benthamiana", tobacco plant that does not recognize EF-Tu, thereby permitting recognition of bacterial EF-Tu thereby confirming EFR as the receptor of EF-Tu. Both  FLS2 and EFR use similar signal transduction pathways to initiate PTI. "A. thaliana" has been instrumental in dissecting these pathways to better understand the regulation of immune responses, the most notable one being the mitogen-activated protein kinase (MAP kinase) cascade. Downstream responses of PTI include callose deposition, the oxidative burst, and transcription of defense-related genes. PTI is able to combat pathogens in a nonspecific manner. A stronger and more specific response in plants is that of effector-triggered immunity (ETI), which is dependent upon the recognition of pathogen effectors, proteins secreted by the pathogen that alter functions in  the host, by plant resistance genes (R-genes), often described as a gene-for-gene relationship. This recognition may occur directly or indirectly via a guardee protein in a hypothesis known as the guard hypothesis. The first R-gene cloned in "A. thaliana" was "RPS2" (resistance to "Pseudomonas syringae" 2), which is responsible for recognition of the effector avrRpt2. The bacterial effector avrRpt2 is delivered into "A. thaliana" via the Type III secretion system of "P. syringae" pv. "tomato" strain DC3000. Recognition of avrRpt2 by RPS2 occurs via the guardee protein RIN4, which is cleaved. Recognition of a pathogen effector  leads to a dramatic immune response known as the hypersensitive response, in which the infected plant cells undergo cell death to prevent the spread of the pathogen. Systemic acquired resistance (SAR) is another example of resistance that is better understood in plants because of research done in "A. thaliana". Benzothiadiazol (BTH), a salicylic acid (SA) analog, has been used historically as an antifungal compound in crop plants. BTH, as well as SA, has been shown to induce SAR in plants. The initiation of the SAR pathway was first demonstrated in "A. thaliana" in which increased SA levels are recognized by  nonexpresser of PR genes 1 ("NPR1") due to redox change in the cytosol, resulting in the reduction of "NPR1. NPR1", which usually exists in a multiplex (oligomeric) state, becomes monomeric (a single unit) upon reduction. When NPR1 becomes monomeric, it translocates to the nucleus, where it interacts with many TGA transcription factors, and is able to induce pathogen-related genes such as "PR1". Another example of SAR would be the research done with transgenic tobacco plants, which express bacterial salicylate hydroxylase, nahG gene, requires the accumulation of SA for its expression Although not directly immunological, intracellular transport affects susceptibility by  incorporating - or being tricked into incorporating - pathogen particles. For example, the "Dynamin-related protein 2b/drp2b" gene helps to move invaginated material into cells, with some mutants increasing "PstDC3000" virulence even further. Evolutionary aspect of plant-pathogen resistance. Plants are affected by multiple pathogens throughout their lifetimes. In response to the presence of pathogens, plants have evolved receptors on their cell surfaces to detect and respond to pathogens. "Arabidopsis thaliana" is a model organism used to determine specific defense mechanisms of plant-pathogen resistance. These plants have special receptors on their cell surfaces that allow for detection of pathogens and  initiate mechanisms to inhibit pathogen growth. They contain two receptors, FLS2 (bacterial flagellin receptor) and EF-Tu (bacterial EF-Tu protein), which use signal transduction pathways to initiate the disease response pathway. The pathway leads to the recognition of the pathogen causing the infected cells to undergo cell death to stop the spread of the pathogen. Plants with FLS2 and EF-Tu receptors have shown to have increased fitness in the population. This has led to the belief that plant-pathogen resistance is an evolutionary mechanism that has built up over generations to respond to dynamic environments, such as increased  predation and extreme temperatures. "A. thaliana" has also been used to study SAR. This pathway uses benzothiadiazol, a chemical inducer, to induce transcription factors, mRNA, of SAR genes. This accumulation of transcription factors leads to inhibition of pathogen-related genes. Plant-pathogen interactions are important for an understanding of how plants have evolved to combat different types of pathogens that may affect them. Variation in resistance of plants across populations is due to variation in environmental factors. Plants that have evolved resistance, whether it be the general variation or the SAR variation, have been able to live longer and hold  off necrosis of their tissue (premature death of cells), which leads to better adaptation and fitness for populations that are in rapidly changing environments. In the future, comparisons of the pathosystems of wild populations + their coevolved pathogens with wild-wild hybrids of known parentage may reveal new mechanisms of balancing selection. In life history theory we may find that "A. thaliana" maintains certain alleles due to pleitropy between plant-pathogen effects and other traits, as in livestock. Research in "A. thaliana" suggests that the immunity regulator protein family EDS1 in general co-evolved with the CC family of nucleotide -bindingleucine-rich-repeat-receptors (NLRs). Xiao et al. 2005 have shown that the powdery mildew immunity mediated by "A. thaliana"s RPW8 (which has a CC domain) is dependent on two members of this family: "EDS1" itself and "PAD4". "RESISTANCE TO PSEUDOMONAS SYRINGAE 5/RPS5" is a disease resistance protein which guards "AvrPphB SUSCEPTIBLE 1/PBS1". "PBS1", as the name would suggest, is the target of "AvrPphB", an effector produced by "Pseudomonas syringae" pv. "phaseolicola". Other research. Ongoing research on "A. thaliana" is being performed on the International Space Station by the European Space Agency. The goals are to study the  growth and reproduction of plants from seed to seed in microgravity. Plant-on-a-chip devices in which "A. thaliana" tissues can be cultured in semi-"in vitro" conditions have been described. Use of these devices may aid understanding of pollen-tube guidance and the mechanism of sexual reproduction in "A. thaliana." Self-pollination. "A. thaliana" is a predominantly self-pollinating plant with an outcrossing rate estimated at less than 0.3%. An analysis of the genome-wide pattern of linkage disequilibrium suggested that self-pollination evolved roughly a million years ago or more. Meioses that lead to self-pollination are unlikely  to produce significant beneficial genetic variability. However, these meioses can provide the adaptive benefit of recombinational repair of DNA damages during formation of germ cells at each generation. Such a benefit may have been sufficient to allow the long-term persistence of meioses even when followed by self-fertilization. A physical mechanism for self-pollination in "A. thaliana" is through pre-anthesis autogamy, such that fertilisation takes place largely before flower opening.