Instruct: Given a question, retrieve relevant passages that answer the question.
Query: How many petals does the Arabidopsis thaliana get?
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.
"A. thaliana" quickly became an important model for the study of plant small RNAs.
The "argonaute1" mutant, named for its resemblance to an "Argonauta" octopuses, was the namesake for the Argonaute protein family central to silencing.
Forward genetic screens focused on vegetative phase change uncovered many genes controlling small RNA biogenesis.
"A. thaliana" became an important model for RNA-directed RNA methylation (transcriptional silencing), partly because many "A. thaliana" methylation mutants are viable, which is not the case for several model animals (in which such mutations cause lethality).
Many gene-for-gene relationships have been identified using the two model organisms, "P. syringae" pv. tomato strain DC3000 and "Arabidopsis". The gene-for-gene relationship describes the recognition of pathogenic avirulence ("avr") genes by host resistance genes (R-genes). "P. syringae" pv. tomato DC3000 is a useful tool for studying "avr": R-gene interactions in "A. thaliana" because it can be transformed with "avr" genes from other bacterial pathogens, and furthermore, because none of the endogenous" hops" genes is recognized by "A. thaliana", any observed aver recognition identified using this model can be attributed to recognition of the introduced "avr" by "A. thaliana". The transformation of "P. syringae" pv tomato DC3000 with effectors from other pathogens have led to the identification of many R-genes in "Arabidopsis" to further advance knowledge of plant pathogen interactions.
"A. thaliana" was the first plant for which a high-quality reference genome sequence was determined (see below), and a worldwide research community has developed many other genetic resources and tools.
The experimental advantages of "A. thaliana" have enabled many important discoveries.
These advantages have been extensively reviewed,
as has its role in fundamental discoveries
about the plant immune system,
natural variation,
and other areas.
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, roadside, railway lines, waste ground and other disturbed habitat,[19][21] but due to its limited competitive ability and small size it is not categorized as a noxious weed.[22] Like most Brassicaceae species, A. thaliana is edible by humans as a salad or cooked, but it does not enjoy a widespread use as a spring vegetable.[19]
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 (AIS), established in 1964. The first International Arabidopsis Conference was held in 1965, in Göttingen, Germany.
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. This is, 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.[65][66][67] 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.
As the NSF 2010 project neared completion, there was a perceived decrease in funding agency interest in "A. thaliana", evidenced by the cessation of USDA funding for "A. thaliana" research, the end of NSF funding for The Arabidopsis Information Resource database, and the rise of new genome-sequence-enabled model plant species (including crops).
Nevertheless, "A. thaliana" remains a popular model, and continues to be the subject of intense study using new technologies such as high-throughput short-read sequencing.
Mapping of mutations from forward screens
is increasingly done
with direct genome sequencing,
combined in some cases with bulked segregant analysis
or backcrossing.
"A. thaliana" is a premier model
for studies of natural genetic variation,
including genome-wide association studies.
Short RNA-guided DNA editing with CRISPR tools has been applied to "A. thaliana" since at least 2013.
"Arabidopsis thaliana" has two homologous proteins, AtToc33 and AtToc34 (The "At" stands for "Arabidopsis thaliana"), which are each about 60% identical in amino acid sequence to Toc34 in peas (called "ps"Toc34). AtToc33 is the most common in "Arabidopsis", and it is the functional analogue of Toc34 because it can be turned off by phosphorylation. AtToc34 on the other hand cannot be phosphorylated.
The small size of its genome, and the fact that it is diploid, makes Arabidopsis thaliana useful for genetic mapping and sequencing — with about 135 mega base pairs[33] and five chromosomes, A. thaliana has one of the smallest genomes among plants.[8] It was long thought to have the smallest genome of all flowering plants,[34] 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 61Mbp.[35] It was the first plant genome to be sequenced, completed in 2000 by the Arabidopsis Genome Initiative.[36] The most up-to-date version of the A. thaliana genome is maintained by the Arabidopsis Information Resource (TAIR).[37] Much work has been done to assign functions to its 27,000 genes and the 35,000 proteins they encode.[38] Post-genomic research, such as metabolomics, has also provided useful insights to the metabolism of this species and how environmental perturbations [39] can affect metabolic processes.[40]
Observations of homeotic mutations led to the formulation of the ABC model of flower development by E. Coen and E. Meyerowitz.[52] 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.
The plant was first described in 1577 in the Harz Mountains by Johannes Thal (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, the German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The genus name, Arabidopsis, comes from Greek, meaning "resembling Arabis" (the genus in which Linnaeus had initially placed it).
GAI or Gibberellic-Acid Insensitive is a gene in "Arabidopsis thaliana" which is involved in regulation of plant growth. GAI represses the pathway of gibberellin-sensitive plant growth. It does this by way of its conserved DELLA motif.
Many genes in the flowering time pathway are conserved across all plants studied to date. However, this does not mean that the mechanism of action is similarly conserved. For example, the monocot rice accelerates its flowering in short-day conditions, while "Arabidopsis thaliana", a eudicot, responds to long-day conditions. In both plants, the proteins "CO" and "FT" are present but in "Arabidopsis thaliana" "CO" enhances "FT" production, while in rice the "CO" homolog represses "FT" production, resulting in completely opposite downstream effects.
In 1841, he renamed "Arabis thaliana" as "Arabidopsis thaliana" (L.) Heynh. "Arabidopsis" was the first plant to have its genome sequenced, and is frequently used as a model for understanding the molecular biology of many plant traits, including flower development and light sensing.
Many of the genes involved in this process are conserved across all the plants studied. Sometimes though, despite genetic conservation, the mechanism of action turns out to be different. For example, rice is a short-day plant, while "Arabidopsis thaliana" is a long-day plant. Both plants have the proteins "CO" and "FLOWERING LOCUS T (FT)", but, in "Arabidopsis thaliana", "CO" enhances "FT" production, while in rice, the "CO" homolog represses "FT" production, resulting in completely opposite downstream effects.
Arabidopsis thaliana is a first class model organism and the single most important species
for fundamental research in plant molecular genetics.
As a model organism, the "Arabidopsis thaliana" response to salinity is studied to aid understanding of other more economically important crops.
High concentration of salt in the soil has negative effects on plants. For example, it reduces the yield that crop plants can produce in 7% of the land. On the other side, some plants show adaptations to changes in soil salinity, in that the plant's exposure to salt initiates certain mechanisms for cell osmotic regulation and causes changes in this plant's water obtaining and loss behaviors. One of such plants is the model plant "Arabidopsis thaliana", a member of the Brassicaceae family. "Arabidopsis thaliana" is native to Eurasia and was introduced to some parts of North America. It grows in rocky, sandy and disturbed terrains. It has been found in many studies that "Arabidopsis thaliana" showed enhanced Na and H extrusion from their cells after exposure to high salinity. Part of "Arabidopsis"’ range might have included high salinity soil and the plant started adapting to that.
Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa.[2][3][4][5][6][7] A. thaliana is considered a weed; it is found by roadsides and in disturbed land.
Arabidopsis lyrata is a species of flowering plant in the family Brassicaceae, closely related to the model organism "Arabidopsis thaliana".
In "Arabidopsis thaliana", most histidine phosphotransfer proteins are redundant, positive regulators in cytokinin signaling. Most of the "Arabidopsis thaliana" histidine phosphotransfer proteins have functional overlap and affect many aspects of plant development. AHP4, however, might play a negative role in cytokinin responses.
Helical growth of single cells, as seen in "Phycomyces" (Fungi) and "Nitella" (Characeae), is believed to be caused by a helical arrangement of microfibrils in the cell wall. This was suggested by birefringence analyses of cell walls. In "Arabidopsis thaliana" mutants helical growth is exhibited at the organ level. Mutant analysis strongly supports the idea that cortical microtubules have an important role in controlling the direction of organ expansion in plants. It is not clear how helical growth mutants affect cell wall assembly of "Arabidopsis thaliana".
Helical growth is the expansion of fungal, algal or higher plant cells or organs that leads to twisted growth of plants
Research of Arabidopsis has led to the discovery of how this auxin mediated root response works. In an attempt to discover the role that phytochrome plays in lateral root development, Salisbury et al. (2007) worked with "Arabidopsis thaliana" grown on agar plates. Salisbury et al. used wild type plants along with varying protein knockout and gene knockout Arabidopsis mutants to observe the results these mutations had on the root architecture, protein presence, and gene expression. To do this, Salisbury et al. used GFP fluorescence along with other forms of both macro and microscopic imagery to observe any changes various mutations caused. From these research, Salisbury et al. were able to theorize that shoot located phytochromes alter auxin levels in roots, controlling lateral root development and overall root architecture. In the experiments of van Gelderen et al. (2018), they wanted to see if and how it is that the shoot of "Arabidopsis thaliana" alters and affects root development and root architecture. To do this, they took Arabidopsis plants, grew them in agar gel, and exposed the roots and shoots to separate sources of light. From here, they altered the different wavelengths of light the shoot and root of the plants were receiving and recorded the lateral root density, amount of lateral roots, and the general architecture of the lateral roots. To identify the function of specific photoreceptors, proteins, genes, and hormones, they utilized various Arabidopsis knockout mutants and observed the resulting changes in lateral roots architecture. Through their observations and various experiments, van Gelderen et al. were able to develop a mechanism for how root detection of Red to Far-red light ratios alter lateral root development.
"Arabidopsis thaliana" has a gene called "AGAMOUS" that plays an important role in defining how many petals and sepals and other organs are generated. Mutations in this gene give rise to the floral meristem obtaining an indeterminate fate, and many floral organs keep on getting produced. We have flowers like roses, carnations and morning glory, for example, that have very dense floral organs. These flowers have been selected by horticulturists since long for increased number of petals. Researchers have found that the morphology of these flowers is because of strong mutations in the "AGAMOUS" homolog in these plants, which leads to them making a large number of petals and sepals. Several studies on diverse plants like petunia, tomato, impatiens, maize etc. have suggested that the enormous diversity of flowers is a result of small changes in genes controlling their development.
It is important to understand how plants achieve resistance to protect the world's food production, as well as the agriculture industry. Many model systems have been developed to better understand interactions between plants and bacterial, fungal, oomycete, viral, and nematode pathogens. Arabidopsis thaliana has been a powerful tool for the study of the subdicipline of plant pathology, that is, the interaction between plants and disease-causing pathogens.