Arabidopsis

Arabidopsis

Thale cress (Arabidopsis thaliana)
Scientific classification
Kingdom:	Plantae
Clade:	Tracheophytes
Clade:	Angiosperms
Clade:	Eudicots
Clade:	Rosids
Order:	Brassicales
Family:	Brassicaceae
Genus:	Arabidopsis Heynh. in Holl & Heynh.
Type species
Arabidopsis thaliana L.
Species
See text
Synonyms
Cardaminopsis (C.A.Mey.) Hayek

Arabidopsis (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (Arabidopsis thaliana), one of the model organisms used for studying plant biology and the first plant to have its entire genome sequenced. Changes in thale cress are easily observed, making it a very useful model.

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Hi everybody this is David Lally at the partnership for research and education in plants or prep for short, and I’m here in the prep lab to introduce you to an experiment you’re going to be doing with a little plant called Arabidopsis. In this video I want to tell you about two things, first what is it about this plant that lead scientists all over the world to choose it as their model research plant and second, how is it that we’re going to use this plant to make discoveries about all plants. Arabidopsis is basically a weed, a plant with no obvious benefit, not for food, shelter, medicine or clothing so why do more than 10,000 scientists around the world use this as their model research plant. There are two main reasons, first they’re small and they grow fast. If you look at the plants, you can see that I have six plants in this tiny little pot, and it takes only six weeks from the time I plant the seeds until I can harvest the next generation. That’s nearly half the time it takes to grow corn plants and one-third the time it takes to grow wheat. Scientists want as much data as quickly as possible, so a small, fast growing plant is going to help them make discoveries much more quickly than if they use linger growing crop plants to study. Now before I tell you the other feature that makes Arabidopsis such a good model organism, let me tell you what we hope to accomplish by studying them. Humans depend on plants for nearly everything they need to survive, so when you talk about a plant being juicy or sweet or having useful chemicals or fibers, you’re talking about a plant’s traits, and humans have been selecting the traits they want implants for thousands of years, first by collecting their seeds or shoots and planting them in the next generation and then by combining desirable traits through interbreeding. So when you’re walking through a supermarket today, you’re looking at a history of human choices. Now, in the past century we’ve learned that those traits have passed from generation to generation through genes, but what we don’t know is which genes are associated with each particular plant trait. If we could lean that then we could much more efficiently select the traits that we want in plants. That’s what were really interested in. Influencing the traits of plants to better serve human needs, and that brings us to the second reason Arabidopsis is such great research plant. It’s very convenient to study it genes. Why? Well in part because it has such a tiny genome. A genome is an entire collection of an organism’s genes. Look at this comparison of genome sizes and notice how small the Arabidopsis genome is next to wheat, corn or rice. If we want to understand how a plant’s genes influences its traits, it’s much more efficient to pick a plant that can create those traits with a very small set of genes. Conveniently, it’s easy and inexpensive to change the genes in Arabidopsis. We can turn a gene on, we can turn a gene off, and we can add a completely new gene to the plants. When we genetically alter the plants, we typically call them mutants and the ones that haven’t been genetically altered we call wild type, and we put the wild type and the mutant side by side and we observe what is the effect of the genetic alteration on the plant’s traits. For example, look at these mutant Arabidopsis plants. In this case, the mutant plants have had a gene knocked out or disabled, and if you look more closely you can see that the mutant plants are smaller and a little bit lighter green than the wild type plants. It’s just the beginning but we’ve just made a connection between the gene and the traits that it influences. But genes aren’t the only that influences a plant’s traits. Plants grow out here. Look at this oak tree. It’s probably twice my age and has experienced dozens of winters, springs, summers and falls. It can’t go anywhere. It has to stay right here so if something is not meeting its needs or something that’s bothering it has to acclimate to those changes. The ability to acclimate to changes in its environment is an inherited trait. Inherited traits are based on genes so scientists hypothesized that plants have a whole bunch of genes that are active under specific environmental conditions. Because of this it’s not unusual to knock out a plant gene and not see any difference between the mutant and the wild type plants. If we want to observe a difference we need to grow the plants under conditions that might turn that gene on. For example, what if the function of the gene we’re studying is to help the plants survive drought, then we would need to examine the mutant in wild type plants under drought conditions to see if that genetic alteration in the mutant plants has changed the way they respond to drought. In your Arabidopsis experiment you’re going to grow one set of wild type in mutant plats under standard growth conditions. So you can examine what is the effect of altering that gene on the Arabidopsis plant’s traits. Then you’re going to grow a second set of wild type in mutant plats under environmental conditions that you’ve altered in some way. And in that set you’re going to ask has that altered gene affected the way the Arabidopsis plants respond to that change in environmental conditions like we mentioned before with the drought. In that way, we’re going to try to figure out what the function of the gene that you’re studying is and that’s what were doing with all the Arabidopsis genes were trying to figure out what is the connection between each Arabidopsis gene and the trait that it controls.

Status

Currently, the genus Arabidopsis has nine species and a further eight subspecies recognised. This delimitation is quite recent and is based on morphological and molecular phylogenies by O'Kane and Al-Shehbaz^[1]^[2] and others.

Their findings confirm the species formerly included in Arabidopsis made it polyphyletic. The most recent reclassification moves two species previously placed in Cardaminopsis and Hylandra and three species of Arabis into Arabidopsis, but excludes 50 that have been moved into the new genera Beringia, Crucihimalaya, Ianhedgea, Olimarabidopsis, and Pseudoarabidopsis.

All of the species in Arabidopsis are indigenous to Europe, while two of the species have broad ranges also extending into North America and Asia.

In the last two decades, Arabidopsis thaliana has gained much interest from the scientific community as a model organism for research on numerous aspects of plant biology. The Arabidopsis Information Resource (TAIR) is a curated online information source for Arabidopsis thaliana genetic and molecular biology research, and The Arabidopsis Book^[3] is an online compilation of invited chapters on Arabidopsis thaliana biology. (Note that as of 2013 no further chapters will be published.) In Europe, the model organism resource centre for Arabidopsis thaliana germplasm, bioinformatics and molecular biology resources (including GeneChips) is the Nottingham Arabidopsis Stock Centre (NASC) whilst in North America germplasm services are provided by the Arabidopsis Biological Resource Center (ABRC) based at Ohio State University. The ordering system for ABRC was incorporated into the TAIR database in June 2001 whilst NASC has always (since 1991) hosted its own ordering system and genome browser.

In 1982, the crew of the Soviet Salyut 7 space station grew some Arabidopsis, thus becoming the first plants to flower and produce seeds in space. They had a life span of 40 days.^[4] Arabidopsis thaliana seeds were taken to the Moon on the Chang'e 4 lander in 2019, as part of a student experiment. As of May 2022 Arabidopsis thaliana has successfully been grown in samples of lunar soil.^[5]

Arabidopsis is quite similar to the Boechera genus.

List of species and subspecies

Arabidopsis arenicola (Richardson ex Hook.) Al-Shehbaz, Elven, D.F. Murray & S.I. Warwick — Arctic rock cress (Greenland, Labrador, Nunavut, Québec, Ontario, Manitoba, Saskatchewan)
Arabidopsis arenosa (L.) Lawalrée — sand rock cress
- A. arenosa subsp. arenosa (Europe: native in Austria, Belarus, Bosnia Herzegovina, Bulgaria, Croatia, Czech Republic, NE France, Germany, Hungary, N Italy, Latvia, Lithuania, Macedonia, Poland, Romania, Slovakia, Slovenia, Switzerland, and Ukraine; naturalized in Belgium, Denmark, Estonia, Finland, Netherlands, Norway, Russia and W Siberia, and Sweden; absent in Albania, Greece, C and S Italy, and Turkey)
- A. arenosa subsp. borbasii (E Belgium, Czech Republic, NE France, Germany, Hungary, Poland, Romania, Slovakia, Switzerland, Ukraine, doubtfully occurring in Denmark)
Arabidopsis cebennensis (DC.) (SE France)
Arabidopsis croatica (Schott) (Bosnia, Croatia)
Arabidopsis halleri (L.)
- A. halleri subsp. halleri (Austria, Croatia, Czech Republic, Germany, N and C Italy, Poland, Romania, Slovakia, Slovenia, Switzerland, and S Ukraine. Probably introduced in N France and extinct in Belgium)
- A. halleri subsp. ovirensis (Wulfen) (Albania, Austria, NE Italy, Romania, Slovakia, Slovenia, SW Ukraine, Yugoslavia)
- A. halleri subsp. gemmifera (Matsumura) (Russian Far East, northeastern China, Korea, Japan, and Taiwan)
Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz — sand cress
- A. lyrata subsp. lyrata (NE European Russia, Alaska, Canada (Ontario west into British Columbia), and southeastern and central United States (Vermont south into northern Georgia and Mississippi northward into Missouri and Minnesota))
- A. lyrata subsp. petraea (Linnaeus) O'Kane & Al-Shehbaz (Austria, Czech Republic, England, Germany, Hungary, Iceland, Ireland, N. Italy, Norway, Russia (NW Russia, Siberia and Far East), Scotland, Sweden, Ukraine, boreal North America (Alaska and Yukon). Apparently extinct in Poland)
- A. lyrata subsp. kamchatica (Fischer ex D.C.) O'Kane & Al-Shehbaz (boreal Alaska, Canada (Yukon, Mackenzie District, British Columbia, northern Saskatchewan), Aleutian Islands, eastern Siberia, the Russian Far East, Korea, northern China, Japan and Taiwan)
Arabidopsis neglecta (Schult.) (Carpathian Mountains (Poland, Romania, Slovakia, and adjacent Ukraine))
Arabidopsis pedemontana (Boiss.) (northwestern Italy and presumably extinct in adjacent SW Switzerland)
Arabidopsis suecica (Fries) Norrlin (Fennoscandinavia and the Baltic region)
Arabidopsis thaliana (L.) Heynh. — thale cress (native range almost all Europe to central Asia, now naturalized worldwide)

Reclassified species

The following species previously placed in Arabidopsis are not currently considered part of the genus.

A. bactriana → Dielsiocharis bactriana
A. brevicaulis → Crucihimalaya himalaica
A. bursifolia → Beringia bursifolia
A. campestris → Crucihimalaya wallichii
A. dentata → Murbeckiella pinnatifida
A. drassiana →
A. erysimoides → Erysimum hedgeanum
A. eseptata → Olimarabidopsis umbrosa
A. gamosepala → Neotorularia gamosepala
A. glauca → Thellungiella salsuginea
A. griffithiana → Olimarabidopsis pumila
A. himalaica → Crucihimalaya himalaica
A. huetii → Murbeckiella huetii
A. kneuckeri → Crucihimalaya kneuckeri
A. korshinskyi → Olimarabidopsis cabulica
A. lasiocarpa → Crucihimalaya lasiocarpa
A. minutiflora → Ianhedgea minutiflora
A. mollis → Beringia bursifolia
A. mollissima → Crucihimalaya mollissima
A. monachorum → Crucihimalaya lasiocarpa
A. mongolica → Crucihimalaya mongolica
A. multicaulis → Arabis tibetica
A. novae-anglicae → Neotorularia humilis
A. nuda → Drabopsis nuda
A. ovczinnikovii → Crucihimalaya mollissima
A. parvula → Thellungiella parvula
A. pinnatifida → Murbeckiella pinnatifida
A. pumila → Olimarabidopsis pumila
A. qiranica → Sisymbriopsis mollipila
A. richardsonii → Neotorularia humilis
A. russeliana → Crucihimalaya wallichii
A. salsugineum → Eutrema salsugineum
A. sarbalica → Crucihimalaya wallichii
A. schimperi → Robeschia schimperi
A. stenocarpa → Beringia bursifolia
A. stewartiana → Olimarabidopsis pumila]]
A. stricta → Crucihimalaya stricta]]
A. taraxacifolia → Crucihimalaya wallichii
A. tenuisiliqua → Arabis tenuisiliqua
A. tibetica → Crucihimalaya himalaica
A. tibetica → Arabis tibetica
A. toxophylla → Pseudoarabidopsis toxophylla
A. trichocarpa → Neotorularia humilis
A. trichopoda → Beringia bursifolia
A. tschuktschorum → Beringia bursifolia
A. tuemurnica → Neotorularia humilis
A. verna → Drabopsis nuda
A. virgata → Beringia bursifolia
A. wallichii → Crucihimalaya wallichii
A. yadungensis →

Cytogenetics

Cytogenetic analysis has shown the haploid chromosome number (n) is variable and varies across species in the genus:^[6]

A. thaliana is n=5^[7] and the DNA sequencing of this species was completed in 2001. A. lyrata has n=8 but some subspecies or populations are tetraploid.^[8] Various subspecies A. arenosa have n=8 but can be either 2n (diploid) or 4n (tetraploid).^[9] A. suecica is n=13 (5+8) and is an amphidiploid species originated through hybridization between A. thaliana and diploid A. arenosa.^[10]

A. neglecta is n=8, as are the various subspecies of A. halleri.^[9]

As of 2005, A. cebennensis, A. croatica and A. pedemontana have not been investigated cytologically.

References

^ O'Kane, Steve L.; Al-Shehbaz, Ihsan A. (1997). "A synopsis of Arabidopsis (Brassicaceae)". Novon. 7 (3): 323. doi:10.2307/3391949. JSTOR 3391949.
^ O'Kane, Steve L.; Al-Shehbaz, Ihsan A. (2003). "Phylogenetic position and generic limits of Arabidopsis (Brassicaceae) based on sequences of nuclear ribosomal DNA". Annals of the Missouri Botanical Garden. 90 (4): 603. doi:10.2307/3298545. JSTOR 3298545. S2CID 85316468.
^ "The Arabidopsis Book". American Society of Plant Biologists. 2019-04-13. Retrieved 2021-08-14.
^ "First species of plant to flower in space". Guinness World Records. Retrieved 2017-03-10.
^ Keeter, Bill (2022-05-12). "Scientists Grow Plants in Lunar Soil". NASA. Retrieved 2022-05-13.
^ Al-Shehbaz, Ihsan A.; O'Kane Jr, Steve L. (2002). "Taxonomy and Phylogeny of Arabidopsis (Brassicaceae)". The Arabidopsis Book. Volume 1. Vol. 1. The American Society of Plant Biologists. pp. e0001. doi:10.1199/tab.0001. PMC 3243115. PMID 22303187. {{cite book}}: |journal= ignored (help)
^ Lysak, M. A; Berr, A; Pecinka, A; Schmidt, R; McBreen, K; Schubert, I (2006). "Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species". Proceedings of the National Academy of Sciences. 103 (13): 5224–5229. Bibcode:2006PNAS..103.5224L. doi:10.1073/pnas.0510791103. PMC 1458822. PMID 16549785.
^ Dart, Sara; Kron, Paul; Mable, Barbara K (2004). "Characterizing polyploidy in Arabidopsis lyrata using chromosome counts and flow cytometry". Canadian Journal of Botany. 82 (2): 185. doi:10.1139/b03-134.
^ ^a ^b Joly, Simon; Schmickl, Roswitha; Paule, Juraj; Klein, Johannes; Marhold, Karol; Koch, Marcus A. (2012). "The Evolutionary History of the Arabidopsis arenosa Complex: Diverse Tetraploids Mask the Western Carpathian Center of Species and Genetic Diversity". PLOS ONE. 7 (8): e42691. Bibcode:2012PLoSO...742691S. doi:10.1371/journal.pone.0042691. ISSN 1932-6203. PMC 3411824. PMID 22880083.
^ Jakobsson, Mattias; Hagenblad, Jenny; Tavaré, Simon; SäLl, Torbjörn; Halldén, Christer; Lind-Halldén, Christina; Nordborg, Magnus (2006). "A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers". Molecular Biology and Evolution. 23 (6): 1217–31. doi:10.1093/molbev/msk006. PMID 16549398.

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