slotreck/pickle huggingface dataset:
Phytohormones regulate diverse aspects of plant growth and environmental responses . Recent high-throughput technologies have promoted a more comprehensive profiling of genes regulated by different hormones . However , these omics data generally result in large gene lists that make it challenging to interpret the data and extract insights into biological significance . With the rapid accumulation of theses large-scale experiments , especially the transcriptomic data available in public databases , a means of using this information to explore the transcriptional networks is needed . Different platforms have different architectures and designs , and even similar studies using the same platform may obtain data with large variances because of the highly dynamic and flexible effects of plant hormones ; this makes it difficult to make comparisons across different studies and platforms . Here , we present a web server providing gene set-level analyses of Arabidopsis thaliana hormone responses . GSHR collected 333 RNA-seq and 1,205 microarray datasets from the Gene Expression Omnibus , characterizing transcriptomic changes in Arabidopsis in response to phytohormones including abscisic acid , auxin , brassinosteroids , cytokinins , ethylene , gibberellins , jasmonic acid , salicylic acid , and strigolactones . These data were further processed and organized into 1,368 gene sets regulated by different hormones or hormone-related factors . By comparing input gene lists to these gene sets , GSHR helped to identify gene sets from the input gene list regulated by different phytohormones or related factors . Together , GSHR links prior information regarding transcriptomic changes induced by hormones and related factors to newly generated data and facilities cross-study and cross-platform comparisons ; this helps facilitate the mining of biologically significant information from large-scale datasets . The GSHR is freely available at http://bioinfo.sibs.ac.cn/GSHR/.
Grain quality is an important agricultural trait that is mainly determined by grain size and composition . Here , we characterize the role of the rice transcription factor ( TF ) SALT-RESPONSIVE ERF1 ( SERF1 ) during grain development . Through genome-wide expression profiling and chromatin immunoprecipitation , we found that SERF1 directly regulates RICE PROLAMIN-BOX BINDING FACTOR ( RPBF ) , a TF that functions as a positive regulator of grain filling . Loss of SERF1 enhances RPBF expression resulting in larger grains with increased starch content , while SERF1 overexpression represses RPBF resulting in smaller grains . Consistently , during grain filling , starch biosynthesis genes such as GRANULE-BOUND STARCH SYNTHASEI ( GBSSI ) , STARCH SYNTHASEI ( SSI ) , SSIIIa , and ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT2 ( AGPL2 ) are up-regulated in SERF1 knockout grains . Moreover , SERF1 is a direct upstream regulator of GBSSI . In addition , SERF1 negatively regulates germination by controlling RPBF expression , which mediates the gibberellic acid (GA)-induced expression of RICE AMYLASE1A ( RAmy1A ) . Loss of SERF1 results in more rapid seedling establishment , while SERF1 overexpression has the opposite effect . Our study reveals that SERF1 represents a negative regulator of grain filling and seedling establishment by timing the expression of RPBF .
An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote . We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region . We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones , such as gibberellic acid , and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors . Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well , strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper . By contrast , genes controlling transcriptional regulation , development , and cell division are up-regulated primarily within the embryo proper . Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated . Genes active in the embryo proper , however , are functionally similar to those active in scarlet runner bean and common bean embryo proper regions . We uncovered a set of suspensor- and embryo proper-specific transcription factors ( TFs ) that are shared by all embryos irrespective of morphology , suggesting that they are involved in early differentiation processes common to all plants . Chromatin immunoprecipitation sequencing ( ChIP-Seq ) experiments with scarlet runner bean and soybean WOX9 , an up-regulated suspensor TF , gained entry into a regulatory network important for suspensor development irrespective of morphology .
Isolated thylakoids from halophytic Eutrema salsugineum ( Thellungiella salsuginea ) produces more H2O2 in comparison to glycophytic Arabidopsis thaliana . The first objective of this study was to verify whether this feature is relevant also to the intact chloroplasts and leaves . Enhanced H2O2 levels in chloroplasts and leaves of E. salsugineum were positively verified with several methods ( electron microscopy , staining with Amplex Red and with diaminobenzidine ) . This effect was associated with a decreased ratio of [ Formula : see text]/H2O2 in E. salsugineum in comparison to A. thaliana as detected by electron paramagnetic resonance method . As a next step , we tested how this specific ROS signature of halophytic species affects the antioxidant status and down-stream components of ROS signaling . Comparison of enzymatic antioxidants revealed a decreased activity of ascorbate peroxidase ( APX ) , enhanced activity of glutathione peroxidase , and the presence of thylakoid-bound forms of iron superoxide dismutase ( FeSOD ) and APX in E. salsugineum . These cues were , however , independent from application of salt stress . The typical H2O2-dependent cellular responses , namely the levels of glucosinolates and stress-related hormones were determined . The total glucosinolate content in E. salsugineum water-treated leaves was higher than in A. thaliana and increased after salinity treatment . Treatment with salinity up-regulated all of tested stress hormones , their precursors and catabolites [ abscisic acid ( ABA ) , dihydrophaseic acid , phaseic acid , 1-aminocyclopropane-1-carboxylic acid , salicylic acid , jasmonic acid , cis-(+)-12-oxo-phytodienoic acid and jasmonoyl-L-isoleucine ] in A. thaliana , whereas in E. salsugineum only a stimulation in ethylene synthesis and ABA catabolism was noted . Obtained results suggest that constitutively enhanced H2O2 generation in chloroplasts of E. salsugineum might be a crucial component of stress-prepardeness of this halophytic species . It shapes a very efficient antioxidant protection ( in which glucosinolates might play a specific role ) and a fine tuning of hormonal signaling to suppress the cell death program directed by jasmonate pathway .
Genetic and biochemical dissection of signaling pathways regulating plant pathogen defense has revealed remarkable similarities with the innate immune system of mammals and Drosophila . Numerous plant proteins resembling eukaryotic receptors have been implicated in the perception of pathogen-derived signal molecules . Receptor-mediated changes in levels of free calcium in the cytoplasm and production of reactive oxygen species and nitric oxide constitute early events generally observed in plant-pathogen interactions . Positive and negative regulation of plant pathogen defense responses has been attributed to mitogen-activated protein kinase cascades . In addition , salicylic acid , jasmonic acid and ethylene are components of signaling networks that provide the molecular basis for specificity of plant defense responses . This article reviews recent advances in our understanding of early signaling events involved in the establishment of plant disease resistance .
Both gibberellic acid and abscisic acid inhibit the light induced synthesis of amaranthin in Amaranthus tricolor seedlings . The auxin , indolyl-3-acetic acid has no effect . The protein/RNA inhibitors , cycloheximide and 8-azaguanine , also reduced the levels of amaranthin produced .
The potassium ion ( K+ ) is vital for plant growth and development , and K+-deprivation leads to reduced crop yields . Here we describe phenotypic , transcriptomic , and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis ( Arabidopsis thaliana ) Columbia . We showed effects on root architecture are mediated through a reduction in cell division in the lateral root ( LR ) meristems , the rate of LR initiation is reduced but LR density is unaffected , and primary root growth is reduced only slightly . This was primarily regulated through gibberellic acid ( GA ) signaling , which leads to the accumulation of growth-inhibitory DELLA proteins . The short LR phenotype was rescued by exogenous application of GA but not of auxin or by the inhibition of ethylene signaling . RNA-seq analysis showed upregulation by K+-deprivation of the transcription factors JUNGBRUNNEN1 ( JUB1 ) and the C-repeat-binding factor (CBF)/dehydration-responsive element-binding factor 1 regulon , which are known to regulate GA signaling and levels that regulate DELLAs . Transgenic overexpression of JUB1 and CBF1 enhanced responses to K+ stress . Attenuation of the reduced LR growth response occurred in mutants of the CBF1 target gene SFR6 , implicating a role for JUB1 , CBF1 , and SFR6 in the regulation of LR growth in response to K+-deprivation via DELLAs . We propose this represents a mechanism to limit horizontal root growth in conditions where K+ is available deeper in the soil .
Jasmonates ( JAs ) are signals in plant stress responses and development . One of the first observed and prominent responses to JAs is the induction of biosynthesis of different groups of secondary compounds . Among them are nicotine , isoquinolines , glucosinolates , anthocyanins , benzophenanthridine alkaloids , artemisinin , and terpenoid indole alkaloids ( TIAs ) , such as vinblastine . This brief review describes modes of action of JAs in the biosynthesis of anthocyanins , nicotine , TIAs , glucosinolates and artemisinin . After introducing JA biosynthesis , the central role of the SCF(COI1)-JAZ co-receptor complex in JA perception and MYB-type and MYC-type transcription factors is described . Brief comments are provided on primary metabolites as precursors of secondary compounds . Pathways for the biosynthesis of anthocyanin , nicotine , TIAs , glucosinolates and artemisinin are described with an emphasis on JA-dependent transcription factors , which activate or repress the expression of essential genes encoding enzymes in the biosynthesis of these secondary compounds . Applied aspects are discussed using the biotechnological formation of artemisinin as an example of JA-induced biosynthesis of secondary compounds in plant cell factories .
Plants are photosynthetic organisms that depend on sunlight for energy . Plants respond to light through different photoreceptors and show photomorphogenic development . Apart from Photosynthetically Active Radiation ( PAR ; 400 - 700 nm ) , plants are exposed to UV light , which is comprised of UV-C ( below 280 nm ) , UV-B ( 280 - 320 nm ) and UV-A ( 320 - 390 nm ) . The atmospheric ozone layer protects UV-C radiation from reaching earth while the UVR8 protein acts as a receptor for UV-B radiation . Low levels of UV-B exposure initiate signaling through UVR8 and induce secondary metabolite genes involved in protection against UV while higher dosages are very detrimental to plants . It has also been reported that genes involved in MAPK cascade help the plant in providing tolerance against UV radiation . The important targets of UV radiation in plant cells are DNA , lipids and proteins and also vital processes such as photosynthesis . Recent studies showed that , in response to UV radiation , mitochondria and chloroplasts produce a reactive oxygen species ( ROS ) . Arabidopsis metacaspase-8 ( AtMC8 ) is induced in response to oxidative stress caused by ROS , which acts downstream of the radical induced cell death ( AtRCD1 ) gene making plants vulnerable to cell death . The studies on salicylic and jasmonic acid signaling mutants revealed that SA and JA regulate the ROS level and antagonize ROS mediated cell death . Recently , molecular studies have revealed genes involved in response to UV exposure , with respect to programmed cell death ( PCD ) .
BACKGROUND AND AIMS : Current strategies for increased crop protection of susceptible tomato plants against pathogen infections include treatment with synthetic chemicals , application of natural pathogen-derived compounds or transfer of resistance genes from wild tomato species within breeding programmes . In this study , a series of 45 genes potentially involved in defence mechanisms was retrieved from the genome sequence of inbred reference tomato cultivar Solanum lycopersicum ' Heinz 1706 ' . The aim of the study was to analyse expression of these selected genes in wild and cultivated tomato plants contrasting in resistance to the biotrophic pathogen Oidium neolycopersici , the causative agent of powdery mildew . Plants were treated either solely with potential resistance inducers or by inducers together with the pathogen . METHODS : The resistance against O. neolycopersici infection as well as RT-PCR-based analysis of gene expression in response to the oomycete elicitor oligandrin and chemical agent β-aminobutyric acid ( BABA ) were investigated in the highly susceptible domesticated inbred genotype Solanum lycopersicum ' Amateur ' and resistant wild genotype Solanum habrochaites . KEY RESULTS : Differences in basal expression levels of defensins , germins , β-1,3-glucanases , heveins , chitinases , osmotins and PR1 proteins in non-infected and non-elicited plants were observed between the highly resistant and susceptible genotypes . Moreover , these defence genes showed an extensive up-regulation following O. neolycopersici infection in both genotypes . Application of BABA and elicitin induced expression of multiple defence-related transcripts and , through different mechanisms , enhanced resistance against powdery mildew in the susceptible tomato genotype . CONCLUSIONS : The results indicate that non-specific resistance in the resistant genotype S. habrochaites resulted from high basal levels of transcripts with proven roles in defence processes . In the susceptible genotype S. lycopersicum ' Amateur ' , oligandrin- and BABA-induced resistance involved different signalling pathways , with BABA-treated leaves displaying direct activation of the ethylene-dependent signalling pathway , in contrast to previously reported jasmonic acid-mediated signalling for elicitins .
Gibberellic acid ( GA(3 ) ) is one of the plant growth regulators which improve salt tolerance and mitigate the salt stress impact on plants . The extant analysis was carried out to study the effect of GA(3 ) and different salt concentrations on seed germination and physiological parameters of oat cultivars . Oats is substantially less tolerant to salt than wheat and barley . Experimentation was conducted as factorial with Completely Randomized Block Design with three replicates . Different concentration of NaCl salt ( ( 25 , 50 , 75 and 100   mM ) were used in test control group and 100 and 150   ppm of GA(3 ) were used in two group by pre-treated ( after 24   h of the seed soaking ) and plants were analyzed on 15th day . Results indicate that increasing salinity would decrease the germination percentage and growth parameter in three oat cultivars . Quotes data indicating a 13 % , 19.9 % and 32.48 % in cultivars NDO-2 , UPO-212 and UPO-94 germination reduction when soil salinity reaches 50   mM. A 36.02 % , 47.33 % and 56.365 reduction in germination is likely when soil salinity reaches 100   mM respectively same cultivars . Seeds treated with GA(3 ) significantly promoted the percentage of germination , shoot and root length , total fresh and dry weight of seedling , tissue water content and seedling vigor index by NDO-2 and UPO-212 under different saline concentration . The maximum average of germination and growth parameters were observed from 150   ppm GA(3 ) treated seeds . But this concentration was significantly inhibited root length in sensitive cultivar UPO-94 at 75 and 100   mM salt as compared to 100   ppm . We observed that , the high concentration of GA(3 ) was not suitable for sensitive oat cultivars . Because the plant root are the real workforce behind any plants success . Thus , it may be concluding that , GA(3 ) treatment could curtail the toxic effect of salinity by increasing germination percentage and shoot and root length , total fresh and dry weight , tissue water content and seedling vigor index in tolerant cultivar .
• Owing to its evolutional plasticity and adaptability , barley ( Hordeum vulgare ) is one of the most widespread crops in the world . Despite this evolutionary success , sexual reproduction of small grain cereals is poorly investigated , making discovery of novel genes and functions a challenging priority . Barley gene Jekyll appears to be a key player in grain development ; however , its role in flowers has remained unknown . • Here , we studied RNAi lines of barley , where Jekyll expression was repressed to different extents . The impact of Jekyll on flower development was evaluated based on differential gene expression analysis applied to anthers and gynoecia of wildtype and transgenic plants , as well as using isotope labeling experiments , hormone analysis , immunogold- and TUNEL-assays and in situ hybridization . • Jekyll is expressed in nurse tissues mediating gametophyte-sporophyte interaction in anthers and gynoecia , where JEKYLL was found within the intracellular membranes . The repression of Jekyll impaired pollen maturation , anther dehiscence and induced a significant loss of fertility . The presence of JEKYLL on the pollen surface also hints at possible involvement in the fertilization process . • We conclude that the role of Jekyll in cereal sexual reproduction is clearly much broader than has been hitherto realized .
Ascochyta blight of lentil is an important fungal disease in many lentil-producing regions of the world causing major yield and grain quality losses . Quick shifts in aggressiveness of the population of the causal agent Ascochyta lentis mandates developing germplasm with novel and durable resistance . In the absence of complete resistance , lentil genotypes CDC Robin and 964a-46 have frequently been used as sources of partial resistance to ascochyta blight and carry non-allelic ascochyta blight resistance genes . RNA-seq analysis was conducted to identify differences in the transcriptome of CDC Robin , 964a-46 and the susceptible check Eston after inoculation with A. lentis . Candidate defense genes differentially expressed among the genotypes had hypothetical functions in various layers of plant defense , including pathogen recognition , phytohormone signaling pathways and downstream defense responses . CDC Robin and 964a-46 activated cell surface receptors ( e.g. receptor like kinases ) tentatively associated with pathogen-associated molecular patterns ( PAMP ) recognition and nucleotide-binding site leucine-rich repeat ( NBS-LRR ) receptors associated with intracellular effector recognition upon A. lentis infection , and differed in their activation of salicylic acid , abscisic acid and jasmonic acid / ethylene signal transduction pathways . These differences were reflected in the differential expression of downstream defense responses such as pathogenesis-related proteins , and genes associated with the induction of cell death and cell-wall reinforcement . A significant correlation between expression levels of a selection of genes based on quantitative real-time PCR and their expression levels estimated through RNA-seq demonstrated the technical and analytical accuracy of RNA-seq for identification of genes differentially expressed among genotypes . The presence of different resistance mechanisms in 964a-46 and CDC Robin indicates their value for pyramiding gene leading to more durable resistance to ascochyta blight .
BACKGROUND : Wheat stem rust , caused by Puccinia graminis f. sp. tritici , is a major wheat disease which is mainly controlled through the release of resistant cultivars containing one or several resistance genes . Considerable effort has been put into the discovery of new resistance genes , but knowledge of their mechanisms of action is often lacking . In this study , the mechanism of resistance conferred by a recently discovered stem rust resistance locus on wheat chromosome 7AL was investigated through microscopic observations and RNA-sequencing , using the susceptible line Columbus and the independent , backcrossed , resistant lines Columbus-NS765 and Columbus-NS766 . RESULTS : Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated 2   days post-inoculation , upon the fungus entry into the plant through the stoma . Resistance was manifested by death of guard and epidermal cells adjacent to an infection site . Occasionally , similar observations were made in the susceptible line , suggesting that the resistance response was the same in all genotypes , but enhanced in the resistant lines . Transcriptomic analysis , combined with assignment of genes to wheat chromosomes , revealed a disproportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A . A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL . Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases . One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus . The results also indicated the presence of a large introgression on chromosome 6A in both resistant lines , but whether it has any role in the resistance response is unclear . CONCLUSIONS : This study represents the first investigation on the resistance mechanism conferred by the wheat 7AL stem rust resistance locus . The resistance response was associated with pre-haustorial cell death , and the transcriptome analysis suggested putative receptor-like cytoplasmic kinases as candidate resistance genes for further investigation .