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Plants adapt to changing environmental conditions by adjusting their growth physiology. Nitrate (NO3-) and ammonium (NH4+) are the major inorganic nitrogen forms for plant uptake. However, high NH4+ inhibits plant growth, and roots undergo striking changes, such as inhibition of cell expansion and division, leading to reduced root elongation. In this work, we show that high NH4+ modulates nitrogen metabolism and root developmental physiology by inhibiting iron (Fe)-dependent Jasmonate (JA) signaling and response in Arabidopsis (Arabidopsis thaliana). Transcriptomic data suggested that NH4+ availability regulates Fe and JA-responsive genes. High NH4+ levels led to enhanced root Fe accumulation, which impaired nitrogen balance and growth by suppressing JA biosynthesis and signaling response. Integrating pharmacological, physiological, and genetic experiments revealed the involvement of NH4+ and Fe-derived responses in regulating root growth and nitrogen metabolism through modulation of the JA pathway during NH4+ stress. The JA signaling transcription factor MYC2 directly bound the promoter of the NITRATE TRANSPORTER 1.1 (NRT1.1) and repressed it to optimize the NH4+/Fe-JA balance for plant adaptation during NH4+ stress. Our findings illustrate the intricate balance between nutrient and hormone-derived signaling pathways that appear essential for optimizing plant growth by adjusting physiological and metabolic responses during NH4+/Fe stress.
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Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.
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Arsénico , Debaryomyces , Oryza , Debaryomyces/genética , Debaryomyces/metabolismo , Oryza/metabolismo , Arsénico/toxicidad , Arsénico/metabolismo , Saccharomyces cerevisiae/genética , Perfilación de la Expresión Génica , Glutatión/metabolismoRESUMEN
Phosphate starvation is one of the major factors limiting plant productivity globally. Soil microflora with an inherent trait of phosphate accumulation directly influences soil phosphorus level by regulating its labile form in soil solution. However, the detailed mechanism involved during their interaction with plants under phosphate deficient conditions is still unexplored. Hence, to dissect these complex gene regulatory networks, transcriptome analysis of A. thaliana roots grown under phosphate starved conditions in presence of phosphate accumulating bacteria (Pseudomonas putida; RAR) was performed. Plants grown under phosphate starved conditions showed upregulation of phosphate starvation responsive genes associated with cell biogenesis, stress, photosynthesis, senescence, and cellular transport. Inoculation of RAR upregulated genes linked to defense, cell wall remodeling, and hormone metabolism in stressed plants. Gene ontology analysis indicated the induction of S-glycoside, glucosinolate, and glycosinolate metabolic processes in RAR inoculated plants under phosphate stressed conditions. Further, protein-protein interaction analysis revealed upregulation of root development, cation transport, anion transport, sulfur compound metabolic process, secondary metabolic process, cellular amino metabolic process, and response to salicylic acid in RAR inoculated plants under phosphate starved conditions. These results indicate the potential role of phosphate accumulating bacteria in alleviating phosphate starvation in plants by involving multiple pathways.
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Arabidopsis , Pseudomonas putida , Arabidopsis/metabolismo , Pseudomonas putida/genética , Pseudomonas putida/metabolismo , Fosfatos/metabolismo , Raíces de Plantas/metabolismo , Perfilación de la Expresión Génica , Suelo , Regulación de la Expresión Génica de las PlantasRESUMEN
MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in regulating various developmental and biological processes. The expression of miRNAs is differentially modulated in response to various biotic and abiotic stresses. Recent findings have shown that some pri-miRNAs encode small regulatory peptides known as microRNA-encoded peptides (miPEPs). miPEPs regulate the growth and development of plants by modulating corresponding miRNA expression; however, the role of these peptides under different stress conditions remains unexplored. Here, we report that pri-miR408 encodes a small peptide, miPEP408, that regulates the expression of miR408, its targets, and associated phenotype in Arabidopsis. We also report that miR408, apart from Plantacyanin (ARPN) and Laccase3 (LAC3), targets a glutathione S-transferase (GSTU25) that plays a role in sulfur assimilation and exhibits a range of detoxification activities with the environmental pollutant. Plants overexpressing miR408 showed severe sensitivity under low sulfur (LS), arsenite As(III), and LS + As(III) stress, while miR408 mutants developed using the CRISPR/Cas9 approach showed tolerance. Transgenic lines showed phenotypic alteration and modulation in the expression of genes involved in the sulfur reduction pathway and affect sulfate and glutathione accumulation. Similar to miR408 overexpressing lines, the exogenous application of synthetic miPEP408 and miPEP408OX lines led to sensitivity in plants under LS, As(III), and combined LS + As(III) stress compared to the control. This study suggests the involvement of miR408 and miPEP408 in heavy metal and nutrient deficiency responses through modulation of the sulfur assimilation pathway.
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Arabidopsis , Arsénico , Fenómenos Biológicos , MicroARNs , Arabidopsis/metabolismo , Arsénico/toxicidad , Arsénico/metabolismo , Estrés Fisiológico/genética , Glutatión/metabolismo , MicroARNs/genética , MicroARNs/metabolismo , Azufre/metabolismo , Regulación de la Expresión Génica de las PlantasRESUMEN
To understand drought tolerance mechanism(s) in clusterbean (Cyamopsis tetragonoloba), we conducted physiological, biochemical, and de novo comparative transcriptome analysis of drought-tolerant (RGC-1002) and drought-sensitive (RGC-1066) genotypes subjected to 30 days of drought stress. Relative water content (RWC) was maintained in tolerant genotype but was reduced in sensitive genotype. Leaf pigment concentrations were higher in tolerant genotype. Net photosynthesis was significantly decreased in sensitive genotype but insignificant reduction was found in tolerant genotype. Enzymatic antioxidant (GR, APX, DHAR) activities were enhanced in tolerant genotype, while there were insignificant changes in these enzymes in sensitive genotype. The ratios of antioxidant molecules (ASC/DHA and GSH/GSSG) were higher in tolerant genotype as compared to sensitive genotype. In sensitive genotype, 6625 differentially expressed genes (DEGs) were upregulated and 5365 genes were downregulated. In tolerant genotype, 5206 genes were upregulated and 2793 genes were downregulated. In tolerant genotype, transketolase family protein, phosphoenolpyruvate carboxylase 3, temperature-induced lipocalin, and cytochrome oxidase were highly upregulated. Moreover, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the drought tolerance may be attributed to upregulated starch and sucrose metabolism-related genes in tolerant genotype. Finally, quantitative real-time PCR confirmed the reproducibility of the RNA-seq data.
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Cyamopsis , Sequías , Antioxidantes/metabolismo , Cyamopsis/genética , Cyamopsis/metabolismo , Mecanismos de Defensa , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genotipo , Reproducibilidad de los Resultados , Estrés Fisiológico/genética , TranscriptomaRESUMEN
Polyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation. IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.
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Arabidopsis/crecimiento & desarrollo , Polifosfatos/metabolismo , Pseudomonas/genética , Pseudomonas/metabolismo , Microbiología del Suelo , Ácido Anhídrido Hidrolasas/genética , Ácido Anhídrido Hidrolasas/metabolismo , Arabidopsis/microbiología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Variación Genética , Ácidos Indolacéticos/metabolismo , Fósforo/metabolismo , Fosfotransferasas (Aceptor del Grupo Fosfato)/genética , Fosfotransferasas (Aceptor del Grupo Fosfato)/metabolismo , Filogenia , Pseudomonas/clasificación , Pseudomonas/enzimología , Rizosfera , Sideróforos/biosíntesis , Suelo/químicaRESUMEN
Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01015-0.
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ClassIII peroxidases are multigene family of plant-specific peroxidase enzyme. They are involved in various physiological and developmental processes like auxin catabolism, cell metabolism, various biotic, abiotic stresses and cell elongation. In the present study, we identified a class III peroxidase (OsPRX38) from rice which is upregulated several folds in both arsenate (AsV) and arsenite (AsIII) stresses. The overexpression of OsPRX38 in Arabidopsis thaliana significantly enhances Arsenic (As) tolerance by increasing SOD, PRX GST activity and exhibited low H2O2, electrolyte leakage and malondialdehyde content. OsPRX38 overexpression also affect the plant growth by increasing total biomass and seeds production in transgenics than WT under As stress condition. Confocal microscopy revealed that the OsPRX38-YFP fusion protein was localized to the apoplast of the onion epidermal cells. In addition, lignification was positively correlated with an increase in cell-wall-associated peroxidase activities in transgenic plants. This study indicates the role of OsPRX38 in lignin biosynthesis, where lignin act as an apoplastic barrier for As entry in root cells leading to reduction of As accumulation in transgenic. Overall the study suggests that overexpression of OsPRX38 in Arabidopsis thaliana activates the signaling network of different antioxidant systems under As stress condition, enhancing the plant tolerance by reducing As accumulation due to high lignification.
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Arabidopsis/metabolismo , Arsénico/metabolismo , Lignina/química , Oryza/enzimología , Peroxidasas/metabolismo , Clonación Molecular , Regulación de la Expresión Génica de las Plantas , Glucanos/química , Peróxido de Hidrógeno/química , Raíces de Plantas/metabolismo , Plantas Modificadas Genéticamente/metabolismo , Salicilamidas/química , Estrés Fisiológico , Regulación hacia ArribaRESUMEN
Cross-kingdom gene regulation by microRNAs (miRNAs) initiated a hot debate on the effective role of orally acquired plant miRNAs on human gene expression. It resulted in the expansion of gene regulation theories and role of plant miRNAs in cross-kingdom regulation of gene expression. This opened up the discussion that 'Whether we really get what we eat?' and 'Whether the orally acquired miRNAs really have a biologically important consequences after entering our digestive and circulatory system?' The reports of orally acquired plant miRNAs inside human alimentary canal have been a topic of discussion in the scientific community. The cross-kingdom gene regulations have raised our hopes to explore the exciting world of plant miRNAs as therapeutic potential and dietary supplements. However, there are reports which have raised concerns over any such cross-kingdom regulation and argued that technical flaws in the experiments might have led to such hypothesis. This review will give the complete understanding of exogenous application and cross-kingdom regulation of plant miRNAs on human health. Here, we provide update and discuss the consequences of plant miRNA mediated cross-kingdom gene regulation and possibilities for this exciting regulatory mechanism as an augmented therapy against various diseases.
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Dietoterapia , MicroARNs/administración & dosificación , Plantas Comestibles/genética , ARN de Planta/administración & dosificación , Animales , Dietoterapia/métodos , Suplementos Dietéticos , Regulación de la Expresión Génica , Humanos , Mamíferos/genética , Interferencia de ARN , ARN Viral , Especificidad de la EspecieRESUMEN
The cotton mealybug Phenacoccus solenopsis is a devastating pest of cotton causing tremendous loss in the yield of crops each year. Widespread physiological and biological studies on P. solenopsis have been carried out, but the lack of genetic information has constrained our understanding of the molecular mechanisms behind its growth and development. To understand and characterize the different developmental stages, RNA-Seq platform was used to execute de-novo transcriptome assembly and differential gene expression profiling for the eggs, first, second, third instar and adult female stages. About 182.67 million reads were assembled into 93,781 unigenes with an average length of 871.4 bp and an N50 length of 1899 bp. These unigenes sequences were annotated and classified by performing NCBI non-redundant (Nr) database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG), Gene ontology (GO), the Swiss-Prot protein database (Swiss-Prot), and nearest related organism Acyrthosiphon pisum (pea aphid) database. To get more information regarding the process of metamorphosis, we performed a pairwise comparison of four developmental stages and obtained 29,415 differentially expressed genes. Some of the differentially expressed genes were associated with functional protein synthesis, anti-microbial protection, development and hormone biosynthesis. Functional pathway enrichment analysis of differentially expressed genes showed the positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study gives a valuable genomics resource of P. solenopsis covering all its developmental stages and will promote future studies on biological processes at the molecular level.
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Perfilación de la Expresión Génica/veterinaria , Hemípteros/crecimiento & desarrollo , Hormonas de Insectos/biosíntesis , Proteínas de Insectos/genética , Animales , Femenino , Regulación del Desarrollo de la Expresión Génica , Ontología de Genes , Hemípteros/genética , Hemípteros/metabolismo , Secuenciación de Nucleótidos de Alto Rendimiento/veterinaria , Análisis de Secuencia de ARN/veterinariaRESUMEN
Arsenic (As) is a ubiquitous metalloid and a health hazard to millions of people worldwide. The presence of As in groundwater poses a threat as it not only affects crop productivity but also contaminates food chain. Therefore, it is essential to understand molecular mechanisms underlying uptake, transport and accumulation of As in plants. In recent past, natural variation in Arabidopsis thaliana has been utilized to understand molecular and genetic adaptation under different stresses. In this study, responses of Arabidopsis accessions were analyzed at biochemical and molecular levels towards arsenate [As(V)] stress. On the basis of reduction in root length, accessions were categorized into tolerant and sensitive ones towards As(V). Root length analysis led to the identification of Col-0 (<10% reduction) and Slavi-1 (>60% reduction) as the most tolerant and sensitive accessions, respectively. Comparative genome-wide expression analysis revealed differential expression of 168 and 548 genes in Col-0 and Slavi-1, respectively, with 120 common differentially expressed genes. A number of genes associated with defense and stress-response, transport system, regulatory mechanisms and biochemical processes showed differential expression in contrasting accessions. The study provides an insight into the molecular mechanisms associated with stress response and processes involved in adaptation strategies towards As stress.
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Adaptación Fisiológica/genética , Arabidopsis/efectos de los fármacos , Arseniatos/toxicidad , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Estrés Fisiológico/genética , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Componentes Aéreos de las Plantas/efectos de los fármacos , Componentes Aéreos de las Plantas/crecimiento & desarrollo , Componentes Aéreos de las Plantas/metabolismo , Raíces de Plantas/efectos de los fármacos , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Transcriptoma/efectos de los fármacosRESUMEN
Steroidal alkaloids (SAs) are widely synthesized and distributed in plants manifesting as natural produce endowed with potential for medicinal, pesticidal and other high-value usages. Glycosylation of these SAs raises complex and diverse glycosides in plant cells that indeed govern numerous functional aspects. During the glycosylation process of these valuable metabolites, the addition of carbohydrate molecule(s) is catalyzed by enzymes known as sterol glycosyltransferases (SGTs), commonly referred to as UGTs, leading to the production of steryl glycosides (SGs). The ratio of SGs and nonglyco-conjugated SAs are different in different plant species, however, their biosynthesis in the cell is controlled by different environmental factors. The aim of this review is to evaluate the current SGT enzyme research and the functional consequences of glycomodification of SAs on the physiology and plant development, which together are associated with the plant's primary processes. Pharmaceutical, industrial, and other potential uses of saponins have also been discussed and their use in therapeutics has been unveiled by in silico analysis. The field of biotransformation or conversion of nonglycosylated to glycosylated phytosterols by the activity of SGTs, making them soluble, available and more useful for humankind is the new field of interest towards drug therapy.
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Glicosiltransferasas/metabolismo , Esteroles/metabolismo , Alcaloides/metabolismo , Secuencia de Aminoácidos , Evolución Molecular , Glicosiltransferasas/biosíntesis , Glicosiltransferasas/química , Humanos , Desarrollo de la PlantaRESUMEN
Azadirachta indica A. Juss, commonly known as Neem, is the reservoir of triterpenoids of economic importance. Metabolite analysis of different developmental stages of leaf and fruit suggests tissue-specific accumulation of the major triterpenoids in this important tree. Though biosynthesis of these complex molecules requires substrate flux from the isoprenoid pathway, enzymes involved in late biosynthetic steps remain uncharacterized. We established and analyzed transcriptome datasets from leaf and fruit and identified members of gene families involved in intermediate steps of terpenoid backbone biosynthesis and those related to secondary transformation leading to the tissue-specific triterpenoid biosynthesis. Expression analysis suggests differential expression of number of genes between leaf and fruit and probable participation in the biosynthesis of fruit-specific triterpenoids. Genome-wide analysis also identified members of gene families putatively involved in secondary modifications in late biosynthetic steps leading to the synthesis of highly oxygenated triterpenoids. Expression and molecular docking analyses suggest involvement of specific members of CYP450 family in secondary modifications for the biosynthesis of bioactive triterpenoids. This study generated rich genomic resource and identified genes involved in biosynthesis of important molecules, which will aid in the advancement of tools for functional genomics and elucidation of the biosynthesis of triterpenoid from this important tree.
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Azadirachta/genética , Azadirachta/metabolismo , Vías Biosintéticas/genética , Perfilación de la Expresión Génica , Genes de Plantas , Metabolómica , Triterpenos/metabolismo , Sistema Enzimático del Citocromo P-450/genética , Frutas/genética , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Limoninas/biosíntesis , Simulación del Acoplamiento Molecular , Anotación de Secuencia Molecular , Familia de Multigenes , Filogenia , Fitoquímicos/análisis , Hojas de la Planta/genética , Metabolismo Secundario/genética , Triterpenos/químicaRESUMEN
Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution. Overall, 65 DHNs were identified by a genome-wide survey of 11 rice species, and 3 DHNs were found to be highly conserved. The correlation of a conserved pattern of DHNs with domestication and diversification of wild to cultivated rice was validated by synonymous substitution rates, indicating that Oryza rufipogon and Oryza sativa ssp. japonica follow an adaptive evolutionary pattern; whereas Oryza nivara and Oryza sativa ssp. indica demonstrate a conserved evolutionary pattern. A comprehensive analysis of tissue-specific expression of DHN genes in japonica and their expression profiles in normal and PEG (poly ethylene glycol)-induced dehydration stress exhibited a spatiotemporal expression pattern. Their interaction network reflects the cross-talk between gene expression and the physiological processes mediating adaptation to dehydration stress. The results obtained strongly indicated the importance of DHNs, as they are conserved during the course of domestication.
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Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Duplicación Cromosómica , Cromosomas de las Plantas , Secuencia Conservada , Productos Agrícolas/genética , Productos Agrícolas/metabolismo , Bases de Datos Genéticas , Deshidratación/genética , Deshidratación/metabolismo , Domesticación , Evolución Molecular , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas/genética , Regulación de la Expresión Génica de las Plantas/fisiología , Modelos Moleculares , Péptido PHI , Raíces de Plantas/metabolismo , Polietilenglicoles , Conformación Proteica , Reacción en Cadena en Tiempo Real de la Polimerasa , Alineación de Secuencia , Homología de Secuencia de AminoácidoRESUMEN
Condensed tannin (CT) or proanthocyanidin (PA) is a unique group of phenolic metabolite with high molecular weight with specific structure. It is reported that, the presence of high-CT in the legumes adversely affect the nutrients in the plant and impairs the digestibility upon consumption by animals. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one of the promising underutilized legume with high protein and oil-content. One of the reasons for its underutilization is due to the presence of CT. Transcriptome sequencing of leaves of two diverse CT-containing lines of P. tetragonolobus was carried out on Illumina Nextseq 500 sequencer to identify the underlying genes and contigs responsible for CT-biosynthesis. RNA-Seq data generated 102586 and 88433 contigs for high (HCTW) and low CT (LCTW) lines of P. tetragonolobus, respectively. Based on the similarity searches against gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) database revealed 5210 contigs involved in 229 different pathways. A total of 1235 contigs were detected to differentially express between HCTW and LCTW lines. This study along with its findings will be helpful in providing information for functional and comparative genomic analysis of condensed tannin biosynthesis in this plant in specific and legumes in general.
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Fabaceae/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Hojas de la Planta/genética , Proantocianidinas/metabolismo , Transcriptoma/genética , Vías Biosintéticas/genética , Cromatografía Líquida de Alta Presión , Mapeo Contig , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Genes de Plantas , Repeticiones de Microsatélite/genética , Anotación de Secuencia Molecular , Proantocianidinas/biosíntesis , ARN Mensajero/genética , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Análisis de Secuencia de ARN , Factores de Transcripción/metabolismoRESUMEN
Chickpea (C. arietinum L.) is an important pulse crop in Asian and African countries that suffers significant yield losses due to attacks by insects like H. armigera. To obtain insights into early responses of chickpea to insect attack, a transcriptomic analysis of chickpea leaves just 20 minutes after simulated herbivory was performed, using oral secretions of H. armigera coupled with mechanical wounding. Expression profiles revealed differential regulation of 8.4% of the total leaf transcriptome with 1334 genes up-regulated and 501 down-regulated upon wounding at log2-fold change (|FC| ≤ -1 and ≥1) and FDR value ≤ 0.05. In silico analysis showed the activation of defenses through up-regulation of genes of the phenylpropanoid pathway, pathogenesis, oxidases and CYTP450 besides differential regulation of kinases, phosphatases and transcription factors of the WRKY, MYB, ERFs, bZIP families. A substantial change in the regulation of hormonal networks was observed with up-regulation of JA and ethylene pathways and suppression of growth associated hormone pathways like GA and auxin within 20 minutes of wounding. Secondary qPCR comparison of selected genes showed that oral secretions often increased differential expression relative to mechanical damage alone. The studies provide new insights into early wound responses in chickpea.
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Cicer/genética , Ciclopentanos/metabolismo , Etilenos/metabolismo , Redes Reguladoras de Genes/genética , Giberelinas/metabolismo , Herbivoria/fisiología , Ácidos Indolacéticos/metabolismo , Oxilipinas/metabolismo , Reguladores del Crecimiento de las Plantas/metabolismo , Animales , Cicer/inmunología , Regulación hacia Abajo/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Mariposas Nocturnas/fisiología , Hojas de la Planta/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Reproducibilidad de los Resultados , Saliva/metabolismo , Análisis de Secuencia de ARN , Transcriptoma/genética , Regulación hacia Arriba/genéticaRESUMEN
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.
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Simulación por Computador , Genes de Plantas , Reguladores del Crecimiento de las Plantas/genética , Proteínas de Plantas/genética , Polimorfismo de Nucleótido Simple , Solanum lycopersicum/genética , Especificidad de la EspecieRESUMEN
Ripening in mango is under a complex control of ethylene. In an effort to understand the complex spatio-temporal control of ripening we have made use of a popular N. Indian variety "Dashehari" This variety ripens from the stone inside towards the peel outside and forms jelly in the pulp in ripe fruits. Through a combination of 454 and Illumina sequencing, a transcriptomic analysis of gene expression from unripe and midripe stages have been performed in triplicates. Overall 74,312 unique transcripts with ≥1 FPKM were obtained. The transcripts related to 127 pathways were identified in "Dashehari" mango transcriptome by the KEGG analysis. These pathways ranged from detoxification, ethylene biosynthesis, carbon metabolism and aromatic amino acid degradation. The transcriptome study reveals differences not only in expression of softening associated genes but also those that govern ethylene biosynthesis and other nutritional characteristics. This study could help to develop ripening related markers for selective breeding to reduce the problems of excess jelly formation during softening in the "Dashehari" variety.
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Frutas/crecimiento & desarrollo , Frutas/genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genes de Plantas , Mangifera/crecimiento & desarrollo , Mangifera/genética , Pared Celular/genética , Etilenos/biosíntesis , Ontología de Genes , Anotación de Secuencia Molecular , Pigmentación/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Reproducibilidad de los Resultados , Transducción de Señal/genéticaRESUMEN
AP2/ERF domain containing transcription factor super family is one of the important regulators in the plant kingdom. The involvement of AP2/ERF family members has been elucidated in various processes associated with plant growth, development as well as in response to hormones, biotic and abiotic stresses. In this study, we carried out genome-wide analysis to identify members of AP2/ERF family in Musa acuminata (A genome) and Musa balbisiana (B genome) and changes leading to neofunctionalisation of genes. Analysis identified 265 and 318 AP2/ERF encoding genes in M. acuminata and M. balbisiana respectively which were further classified into ERF, DREB, AP2, RAV and Soloist groups. Comparative analysis indicated that AP2/ERF family has undergone duplication, loss and divergence during evolution and speciation of the Musa A and B genomes. We identified nine genes which are up-regulated during fruit ripening and might be components of the regulatory machinery operating during ethylene-dependent ripening in banana. Tissue-specific expression analysis of the genes suggests that different regulatory mechanisms might be involved in peel and pulp ripening process through recruiting specific ERFs in these tissues. Analysis also suggests that MaRAV-6 and MaERF026 have structurally diverged from their M. balbisiana counterparts and have attained new functions during ripening.
Asunto(s)
Evolución Biológica , Genoma de Planta , Estudio de Asociación del Genoma Completo , Familia de Multigenes , Musa/genética , Proteínas de Plantas/genética , Factor de Transcripción AP-2/genética , Secuencias de Aminoácidos , Mapeo Cromosómico , Análisis por Conglomerados , Secuencia Conservada , Etilenos/farmacología , Evolución Molecular , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Variación Genética , Modelos Moleculares , Musa/clasificación , Especificidad de Órganos/genética , Filogenia , Regiones Promotoras Genéticas , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas , Elementos de Respuesta , Factor de Transcripción AP-2/químicaRESUMEN
Opium poppy (Papaver somniferum L.), known for biosynthesis of several therapeutically important benzylisoquinoline alkaloids (BIAs), has emerged as the premier organism to study plant alkaloid metabolism. The most prominent molecules produced in opium poppy include narcotic analgesic morphine, the cough suppressant codeine, the muscle relaxant papaverine and the anti-microbial agent sanguinarine and berberine. Despite several health benefits, biosynthesis of some of these molecules is very low due to tight temporal and spatial regulation of the genes committed to their biosynthesis. Transcription factors, one of the prime regulators of secondary plant product biosynthesis, might be involved in controlled biosynthesis of BIAs in P. somniferum. In this study, identification of members of different transcription factor gene families using transcriptome datasets of 10 cultivars of P. somniferum with distinct chemoprofile has been carried out. Analysis suggests that most represented transcription factor gene family in all the poppy cultivars is WRKY. Comparative transcriptome analysis revealed differential expression pattern of the members of a set of transcription factor gene families among 10 cultivars. Through analysis, two members of WRKY and one member of C3H gene family were identified as potential candidates which might regulate thebaine and papaverine biosynthesis, respectively, in poppy.