arabidopsis thaliana google scholar

Below, we sample a few items from the smorgasbord. Other shared informational resources include databases of gene expression (Schmid et al. Bjornson, M., Kajala, K., Zipfel, C. & Ding, P. Low-cost and high-throughput RNA-seq library preparation for Illumina sequencing from plant tissue. conceived and designed the experiments. A. thaliana is often indicated simply by the genus name Arabidopsis, even though other species within the genus also are subjects of investigation. The transcriptional landscape of Arabidopsis thaliana pattern - Nature Each gene repressed in this study was plotted according to the time it is first repressed (panels from top to bottom), the number of tested patterns which repress it (x axis) and the number of abiotic stresses in the AtGenExpress dataset which also repress it within the first 3 h (y axis). Bioinformatics 31, 37183720 (2015). Many biological processes were first discovered in Arabidopsis (Provart et al. 2016). Sci. Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R. & Pfister, H. Upset: visualization of intersecting sets. You are using a browser version with limited support for CSS. Google Scholar. Wild-type tomatoes of the Micro-Tom variety are red (top). J. Biol. We thank P. Ding for sharing protocols and material related to Tn-5 tagmentation, S. Ranf for providing the sd1-29 mutant and 3-OH-FA pattern prior to publication, G. Stacey for providing the lyk4/5 mutant, C. J. S. Moreira for assistance in genotyping the glr2.72.82.9 CRISPR line, and past and present members of the Zipfel laboratory for helpful discussions. Shao, Q., Gao, Q., Lhamo, D., Zhang, H. & Luan, S. Two glutamate- and pH-regulated Ca2+ channels are required for systemic wound signaling in Arabidopsis. The graph plots the number of publications since 1945 featuring selected model organisms gathered from PubMed (NCBI Resource Coordinators 2017) searches using full genus and species names as search terms. Each point represents one stoma, and plot represents stomata from a total of 12 plants assayed over 5 experiments (n=36-178 stomata per genotype/treatment/experiment). Empirical analysis of transcriptional activity in the. Evol. A wealth of Arabidopsis tools, resources, and shared experiences facilitate efficient generation of data and new understanding. 2010). c, The top BLAST hit for each exon of AT3G032090 are shown, with strong similarity to WRKY40 (AT1G80840) in the expressed exon of AT3G032090. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in. Genome Res. Toyota, M. et al. and M.B. Leaves of most plants are decorated with trichomes, or leaf hairs. Figure modified from Paterson et al. Arabidopsis thaliana articles from across Nature Portfolio. Hohmann N., Wolf E. M., Lysak M. A., Koch M. A., 2015. Weaker selection on genes with treatment-specific expression consistent Image modified from Zhang et al. Wild-type Arabidopsis flowers consist of four floral whorls: 1 - sepals (se), 2 - petals (pe), 3 - stamens (st), and 4 - carpels (ca), shown in panel A. Sepals result from the combined activity of A and E genes; petals from B, A, and E genes, stamens from B, C, and E genes, and carpels from C and E genes. (2008). Pattanaik S., Patra B., Singh S. K., Yuan L., 2014. 2000); reduced GL3 expression results in few trichomes, whereas overexpression increases trichome density (Figure 4). 14, R36 (2013). 63, 27692786 (2012). Timofeev-Resovskii N. V., Ginter E. K., Glotov N. V., Ivanov V. I., 1971. Chromosoma. The potential fusion protein does not encode any transmembrane domains. Arabidopsis research was key to developing the ABCE model of floral development (Figure 3). A gateway cloning vector set for high-throughput functional analysis of genes in planta. Arabidopsis genes newly identified through mutant analysis are named for the mutant phenotype (Meinke and Koornneef 1997), whereas those identified via reverse genetics are often named for the encoded protein. ROS and JA signaling participate in positive regulation of Pyrus betulifolia LysM-containing receptor protein 1 (PbeLYP1) in Valsa canker resistance, A general non-self response as part of plant immunity. Zhao C., Johnson B. J., Kositsup B., Beers E. P., 2000. Yu, X., Feng, B., He, P. & Shan, L. From chaos to harmony: responses and signaling upon microbial pattern recognition. 2c. Plant Cell 21, 972984 (2009). Gene names are typically abbreviated to three letters. Yang, Y., Costa, A., Leonhardt, N., Siegel, R. S. & Schroeder, J. I. eLife 3, e03766 (2014). 4. ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Kebeish R., Niessen M., Thiruveedhi K., Bari R., Hirsch H.-J., et al., 2007. Google Scholar. Neighboring genes shown in black. Plant Physiol. 3 Complete complement of set sizes among collapsed pattern-induced and pattern-repressed gene sets. 93, 592613 (2018). The radicle (embryonic root) had emerged from the testa (seed coat) by 3 days. d, WRKY40 is strongly expressed (note y axis) and strongly pattern-induced. However, seeds on the soil surface are susceptible to desiccation, and plastic domes or tented plastic wrap can be used to reduce evaporation for the first week or longer. Partnership for research & education in plants (PREP): involving high school students in authentic research in collaboration with scientists. Laboratory exercises to introduce gravitropism. 14, 234240 (2004). Z., Weise S. E., Kiss H. G., 2000. Article 2018;210(2):607-19. We apologize to the many Arabidopsis researchers whose work we could not highlight in this sampling because of length limitations. Arabidopsis thaliana could have easily escaped human scrutiny. Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. 1998). Cell Host Microbe 21, 518529 (2017). Kutschera, A. et al. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. In a fascinating parallel, auxin and jasmonate (jasmonoyl-l-isoleucine) molecules bind between the F-box protein and the targeted repressor, stabilizing the interaction to ensure target protein ubiquitination and degradation (Tan et al. Reverse-genetics mutants carrying T-DNA insertions in genes essential for autophagy (atg mutants) fail to recover from the return to light after extended darkness. Our research is funded by faculty development grants from The University of Mary Hardin-Baylor Provost (to A.W.W. 2016). Some plant cell structures, such as trichomes and chloroplasts, differ in Arabidopsis as well. Yamada K., Lim J., Dale J. M., Chen H., Shinn P., et al., 2003. Importantly, the definition of a small subset of core immunity response genes common and specific to pattern response revealed the function of previously uncharacterized GLUTAMATE RECEPTOR-LIKE (GLR) calcium-permeable channels in immunity. and M.B. Arabidopsis is almost uniquely suited for undergraduate research projects. High school and college students have successfully employed Arabidopsis to explore gravitropism (Kiss et al. Large Scale Genomic Rearrangements in Selected Arabidopsis thaliana T-DNA Lines Are Caused by T-DNA Insertion Mutagenesis. Nature 457, 11541158 (2009). In (b), each point represents peak ratio of YFP to CFP (proportional to Ca2+ concentration) for a single seedling, normalized to initial ratio. *Department of Biology, University of Mary Hardin-Baylor, Belton, Texas 76513, Department of BioSciences, Rice University, Houston, Texas 77005. Moreover, the high complementarity between plant miRNAs and their targets allowed systematic, high-confidence miRNA target identification (Rhoades et al. Ossowski S., Schneeberger K., Lucas-Lled J. I., Warthmann N., Clark R. M., et al., 2010. Hamamura Y., Saito C., Awai C., Kurihara D., Miyawaki A., et al., 2011. Plant development is plastic and modular, tolerating many experimental insults. Phylogenetic distribution and evolution of mycorrhizas in land plants. USA 103, 1010410109 (2006). Figure modified from Krizek and Fletcher (2005). Open Access Karrikins discovered in smoke trigger Arabidopsis seed germination by a mechanism requiring gibberellic acid synthesis and light. Among induced genes, for each pattern a specificity measure (expression in response to pattern/total expression in experiment) was calculated, and genes with at least one SPM>0.33 (one pattern treatment responsible for approximately 1/3 total expression in study, n=412) were gathered. Saijo, Y., Loo, E. P.-I. Full-length complementary DNAs for most genes (Yamada et al. 2015). In this model, E-class genes are needed for all floral structures. Analysis of the genome sequence of the flowering plant. R package version 1.5.4 (2020). Nelson D. C., Riseborough J.-A., Flematti G. R., Stevens J., Ghisalberti E. L., et al., 2009. Thus, the gene has a similar impact on this crop plant as was first demonstrated in Arabidopsis. Navarro, L. et al. Dra-3 originates from Dravla (Sweden; Latitude 62.68 . 1995; Tanksley and Mccouch 1997). & Zhang, B. Instead, Arabidopsis has become the most widely studied plant in modern biology despite its absence from the dinner table. Matsushima R., Tang L. Y., Zhang L., Yamada H., Twell D., et al., 2011. & Mohnen, D. Pectins: structure, biosynthesis, and oligogalacturonide-related signaling. Krysan P. J., Young J. C., Tax F., Sussman M. R., 1996. and JavaScript. In this example, the numeral one denotes the first mutant isolated in the transport inhibitor response mutant screen. Among other fascinating processes, the complex dance of the alternation of generations is subject to dissection in Arabidopsis. & Dehesh, K. Determinants of timing and amplitude in the plant general stress response. Remarkable processes occur at the cellular level, also. Leaf epidermal development: A gene regulating Arabidopsis trichome density. USA 106, 1884318848 (2009). (C) In the absence of B-gene activity, only sepals and carpels form. Unlike animal model organisms for which the preservation of lineages often involves uninterrupted ongoing work, Arabidopsis seeds can survive for years without attention at room temperature and even longer with refrigeration. A comparative study of the Arabidopsis thaliana guard-cell transcriptome and its modulation by sucrose. Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in. Extended Data Fig. Biol. A, B, and E activity yields petals. 5 Pattern-triggered transcriptional repression acts in time-resolved waves. Xiao, S.-J., Zhang, C., Zou, Q. Whereas Wisconsin fast plants have larger structures and fast life cycles (Williams 1997), the wealth of bioinformatics resources, mutants, and published studies that Arabidopsis brings to the classroom is unrivaled. a, b, c, Increase in intracellular Ca2+ concentration in response to treatment in seedlings (a, c) or leaf discs (b). Plant Biol. (B) shows microscopic sections at different developmental stages with DNA stained blue using DAPI. Ranf, S. et al. Perception of the Arabidopsis danger signal peptide 1 involves the pattern recognition receptor AtPEPR1 and its close homologue AtPEPR2. Front. Plant J. This work allowed the discovery of plant-specific roles for autophagy, including recovery from darkness-induced starvation (Figure 7; Phillips et al. Biotechnol. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. Bethesda, MD 20894, Web Policies Figure modified from Phillips et al. Live-cell imaging reveals the dynamics of two sperm cells during double fertilization in. (2014)], Arabidopsis trichomes do not produce the diverse chemical secretions present in many plant species, including tomato, in which glandular trichomes can be investigated (McDowell et al. We would like to show you a description here but the site won't allow us. official website and that any information you provide is encrypted Subcellular research in Arabidopsis: Pollen organellar DNA degradation. (E) In the absence of E-gene activity, no floral structures form, and the numerous whorls resemble leaves (le), including the presence of leaf hairs (trichomes) decorating the surfaces. Plant Microbe Interact. USA 103, 1009810103 (2006). Benn, G. et al. We collated over 27 terabases of RNA-sequencing data on Arabidopsis thaliana from over 300 peer-reviewed studies and 200 treatment conditions to investigate this hypothesis. Expression changes in this study at a, 30 min and b, 3 h are plotted against previously published results for flg22, elf18/26, and chitooctaose (CO8). Phytochemistry 57, 929967 (2001). Article CAS Google Scholar Gupta S, Misra S, Kumar M, Mishra SK, Tiwari S, Narayan S, Agrawal L, Chauhan PS (2022) Enhancement of drought tolerance in transgenic arabidopsis thaliana plants overexpressing chickpea Ca14-3-3 gene. BMC Genomics 15, 431 (2014). (A) Stomata, the two-celled pores that regulate gas exchange, are distributed among interlocked pavement cells in wild type. Arabidopsis plants can develop from a seed to a plant bearing mature seeds in as few as 6 weeks, depending on growth conditions (Figure 1). Article (A) Microspore cells develop into pollen by two rounds of mitosis, producing two sperm cells within a generative cell. Much of the photorespiratory pathway was revealed using Arabidopsis genetics (Somerville 2001). Schlierf A., Altmann E., Quancard J., Jefferson A. Sci. Singh R., Singh S., Parihar P., Singh V. P., Prasad S. M., 2015. Endogenous and silencing-associated small RNAs in plants. The timeline highlights selected events in Arabidopsis history (Thal 1588; Braun 1873; Laibach 1907; Titova 1935; Reinholz 1947; Langridge 1955; McKelvie 1962; Rdei 1975; Somerville and Ogren 1979; Meyerowitz and Pruitt 1985; Lloyd et al. Li J.-F., Norville J. E., Aach J., Mccormack M., Zhang D., et al., 2013. 182, 15821596 (2020). It first produces a compact set of rosette leaves. van Veen, H. et al. To test plant responses to other environmental parameters, some incubators can regulate humidity and atmospheric gases such as carbon dioxide. Arabidopsis data and components have been used in translational projects in crop plants. Lorek, J., Griebel, T., Jones, A. M., Kuhn, H. & Panstruga, R. The role of Arabidopsis heterotrimeric G-protein subunits in MLO2 function and MAMP-triggered immunity. Translational research: Arabidopsis MYB12 increases tomato flavonol content. ), the National Institutes of Health (R01GM079177 to B.B. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in. Comparative genome-wide analysis of WRKY, MADS-box and MYB - Nature In the realm of proteomics, available data include protein sequences (Baerenfaller et al. Glob. Amsterdam Proc. Molecular mechanisms of flower development: an armchair guide. Plants 1, 15140 (2015). OMalley, R. C. et al. Careful cultivation of an obscure garden weed has taught us much about both the garden and the gardener. Sucrose signaling regulates anthocyanin biosynthesis through a MAPK cascade in Arabidopsis thaliana. Chang C., Kwok S. F., Bleecker A. Some authors consider Arabidopsis to be a common name, printing the nonitalicized word with or without capitalization. Sect. Lett. Seeds and seedlings are small enough to germinate by the hundreds on a single Petri dish. Seeds can be germinated directly on the surface of moistened soil. Unlike in animals, the two sperm cells are used for double fertilization to produce both embryo and endosperm tissues in angiosperm plants (Hamamura et al. Among plants, Arabidopsis is small, grows quickly, and flourishes indoors (Figure 1). the contents by NLM or the National Institutes of Health. Wild-type names are written using capital letters; mutant names are lowercase. Hu, X. Y., Neill, S. J., Cai, W. M. & Tang, Z. C. Induction of defence gene expression by oligogalacturonic acid requires increases in both cytosolic calcium and hydrogen peroxide in Arabidopsis thaliana. 2004). Arabidopsis offers insight into a host of other plant developmental and cellular processes. Alternatively, white light can be filtered through colored plastic sheets (Stasinopoulos and Hangarter 1990), or plates can be wrapped in foil to provide darkness. Libault, M., Wan, J., Czechowski, T., Udvardi, M. & Stacey, G. Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. Its small genome size, rapid life cycle . Moss chloroplasts are surrounded by a peptidoglycan wall containing D-amino acids. For example, Beta vulgaris (sugar beet) produces betalains, vivid antioxidants (Brockington et al. Gateway-compatible vectors for plant functional genomics and proteomics. PubMedGoogle Scholar. 25, 10831092 (2012). The ovules of a flower are receptive before the pollen is mature. Scanning electron micrographs of (A) wild-type seedlings or (D) leaves show trichomes (leaf hairs) distributed on the top surface of true leaves (A and D) but not cotyledons (A). Google Scholar. AtMYB12 regulates caffeoyl quinic acid and flavonol synthesis in tomato: expression in fruit results in very high levels of both types of polyphenol. 2008), and ubiquitination (Kim et al. Identification of transferred DNA insertions within. 161, 21462158 (2013). Plant Cell 22, 508522 (2010). ISSN 2055-0278 (online). 43, e47 (2015). Natl Acad. 172, 668689 (2016). Plant Physiol. Reinholz E., 1947. When the Arabis-like genus Arabidopsis was created, the species thaliana was initially retained in Arabis (De Candolle 1824). 2001). A small fraction of mis-aligned reads likely account for the observed pattern AT3G032090. Data were collected every 30 s (a, b), 5 s, or 12 s (c). Kilian J., Whitehead D., Horak J., Wanke D., Weinl S., et al., 2007. B., Assenberg R., et al., 2016. 2002) and validation (Llave et al. d, Pearson correlation heatmap of DESeq2-calculated log2(FC) showing clustering largely by time point, with the strongest correlations at 30 min. 2016), suggesting that the genes are vestiges of a lost peptidoglycan biosynthesis pathway in Arabidopsis. Biochem. The first plant microRNAs (miRNAs) were discovered in Arabidopsis (Llave et al. 1988). How can plants tell which way is up? BMC Genom. Arabidopsis models most typical features and specialized cell types of seed plants, including perfect flowers (perfect referring to the presence of both stamens and carpel; Figure 3), stems, apical meristems, simple leaves, trichomes (defensive leaf hairs; Figure 4), epidermal pavement cells that interlock to form an outer barrier (Figure 5), stomata that open or close to regulate gas exchange between the leaf and atmosphere (Figure 5), roots, root hairs, vascular tissue, pollen (Figure 6), and female gametophytes. S. Diaz et al., Plant trait responses to grazing-a global synthesis. Mol. To modern science, Arabidopsis is a most useful plant. Nitrogen | Free Full-Text | Isoenzymatic Pattern of Hydrogen - MDPI A calmodulin-gated calcium channel links pathogen patterns to plant immunity. The site is secure. One example is the formation of elegant epidermal architecture. Arbuscular mycorrhizal fungi are crucial for nutrient and water absorption and colonize 80% of land plants (Wang and Qiu 2006). 1986; Coen and Meyerowitz 1991; Chang et al. Extended Data Fig. Nature 428, 764767 (2004). 20, 19831992 (2014). The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Beyond the Arabidopsis techniques available to individual research groups, there are useful curated community collections. For example, Charles Darwin and his son Francis conducted pioneering experiments investigating plant phototropismsgrowth toward or away from lightin oat (Avena), canary grass, asparagus, and beet, as well as the Arabidopsis cousins white mustard and Brassica oleracea (Darwin and Darwin 1880). Matching NLR immune receptors to autoimmunity in camta3 mutants using antimorphic NLR alleles. Bohmert K., Camus I., Bellini C., Bouchez D., Caboche M., et al., 1998. Comparing Arabidopsis receptor kinase and receptor protein-mediated immune signaling reveals BIK1-dependent differences. The authors declare no competing interests. 2002). 2005; Kilian et al. Rev. Transcriptomes of eight Arabidopsis thaliana accessions reveal core conserved, genotype- and organ-specific responses to flooding stress. In Flora Londinensis, William Curtis remarked that we have it frequent enough on our walls, and sometimes on dry ground, about town: and it may be found in great abundance on the south side of Greenwich Park Wall No particular virtues or uses are ascribed to it (Curtis 1777). Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Biology 4 Pattern-responsive genes tend to be repressed by single patterns, though there does exist a core set of 93 genes repressed by all tested patterns. Nonetheless, the depth of understanding and ease of manipulation in the Arabidopsis system is unrivaled, and Arabidopsis will remain the reference plant for the foreseeable future. [Google Scholar] For example, the Arabidopsis transcription factor MYB12 stimulates the production of flavonol chemicals (Mehrtens et al. Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. Luo J., Butelli E., Hill L., Parr A., Niggeweg R., et al., 2008. Research using Arabidopsis has greatly expanded our knowledge of plantsthe organisms that provide most human nutrition and atmospheric oxygenand revealed key, common processes in diverse organisms beyond plants. Likewise, the F-box CORONATINE-INSENSITIVE1 (COI1) protein, also discovered through Arabidopsis forward genetics, is a receptor for the jasmonate phytohormone (Sheard et al. Arabidopsis and Populus are dicotyledonous plants; Sorghum and rice are monocots. Isolation and characterization of autophagy-defective mutants of. Sci. Nat. The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in. Earley K. W., Haag J. R., Pontes O., Opper K., Juehne T., et al., 2006. If atmospheric humidity is low, plants may be damaged by sudden removal of the cover, and partially removing the plastic dome or cutting slits in plastic wrap a few days before entirely removing the cover aids survival. Sucrose rescues seedling establishment but not germination of Arabidopsis mutants disrupted in peroxisomal fatty acid catabolism. The receptor role was first discovered for the Arabidopsis TRANSPORT INHIBITOR RESPONSE1 (TIR1) F-box protein that is sufficient to target AUX/IAA transcriptional repressors for degradation in heterologous systems (Dharmasiri et al. Plant J. Phillips A. R., Suttangkakul A., Vierstra R. D., 2008. Plant Sci. 2000). Early descriptions of the plant used aliases. 2005). Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants. 2002), the protrusions from single root epidermal cells that increase root surface area. J. Integr. Mol. Here, we performed a detailed transcriptomic analysis in an early time series focused to study rapid-signalling transcriptional outputs induced by well-characterized patterns in the model plant Arabidopsis thaliana. Like with auxin and jasmonate, the hormones gibberellin and strigolactone also signal through F-box proteins that promote the destruction of repressors in the corresponding pathways (Morffy et al. The top three GO terms for each time point are indicated. HHS Vulnerability Disclosure, Help Compared to most organisms, the metabolic complexity of plants is staggering, offering fertile ground for biochemical research. Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP-triggered immunity. Many modern crops have been subjected to millennia of artificial selection and only bear passing resemblance to their wild relatives (Doebley et al. The dpd1 mutant, defective in an exonuclease, has persistent organellar DNA (plastidial and mitochondrial) through the tricellular stage of development. 2008). 2002). Statistical tests were performed in R, two-way ANOVA blocking by experiment. Natl Acad. Bauwe H., Hagemann M., Fernie A. R., 2010. A locus number follows the letters to distinguish different genes that can mutate to a given phenotype (for genes identified by mutation) or various homologs (for genes identified by homology), and various alleles of the same gene are enumerated following a hyphen. Comparative functional genomic analysis of. This is a preview of subscription content, access via your institution. In this system, the TIR1 gene is At3g62980, indicating that the gene is on chromosome 3 with the large number reflecting a position near the bottom of the chromosome. and transmitted securely. Bacteria were harvested from leaf discs two days post-inoculation; each point represents one plant, and shapes represent three independent experiments (n=6 plants per genotype/treatment/experiment). Conservation of the Restricted Expression of Brassicaceae

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