scholarly journals Transcriptome Reprogramming of Tomato Orchestrate the Hormone Signaling Network of Systemic Resistance Induced by Chaetomium globosum

2021 ◽  
Vol 12 ◽  
Author(s):  
Jagmohan Singh ◽  
Rashmi Aggarwal ◽  
Bishnu Maya Bashyal ◽  
K. Darshan ◽  
Pooja Parmar ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Plant Pathogens ◽  
Biological Control Agent ◽  
Induced Defense ◽  
Chaetomium Globosum ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Hormone Signaling ◽  
Signaling Transduction ◽  
Chlorophyll Metabolism

Chaetomium globosum is a potential biological control agent effective against various plant pathogens. Several reports are available on the mycoparastism and antibiosis mechanisms of C. globosum against plant pathogenic fungi, whereas a few states induced resistance. The potential induced defense component of C. globosum (Cg-2) was evaluated against early blight disease of tomato (Solanum lycopersicum) and further, global RNA sequencing was performed to gain deep insight into its mechanism. The expression of marker genes of hormone signaling pathways, such as PR1, PiII, PS, PAL, Le4, and GluB were analyzed using real-time quantitative reverse transcription PCR (qRT-PCR) to determine the best time point for RNA sequencing. The transcriptome data revealed that 22,473 differentially expressed genes (DEGs) were expressed in tomato at 12 h post Cg-2 inoculation as compared with control plants and among these 922 DEGs had a fold change of −2 to +2 with p < 0.05. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the DEGs were belonging to metabolic pathways, biosynthesis of secondary metabolites, plant–pathogen interaction, chlorophyll metabolism, and plant hormone signal transduction. Gene Ontology (GO) analysis revealed that DEGs were enriched mainly related to binding activity (GO:0005488), catalytic activity (GO:0003824), metabolic process (GO:0008152), cellular process (GO:0009987), response to stimulus (GO:0050896), biological regulation (GO:0065007), and transcription regulator activity (GO:0140110). The gene modulations in hormone signaling transduction, phenylpropanoid biosynthesis, and mitogen-activated protein kinases (MPK) signaling indicated the upregulation of genes in these pathways. The results revealed active participation of jasmonic acid (JA) and salicylic acid (SA) signaling transduction pathways which further indicated the involvement of induced systemic resistance (ISR) and systemic acquired resistance (SAR) in the systemic resistance induced by Cg-2 in tomato.

scholarly journals Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Anastasia Dimopoulou ◽  
Ioannis Theologidis ◽  
Burghard Liebmann ◽  
Kriton Kalantidis ◽  
Nikon Vassilakos ◽  
...  
Keyword(s):  
Plant Defense ◽  
Stress Responses ◽  
Bacillus Amyloliquefaciens ◽  
Plant Pathogens ◽  
Biological Control Agent ◽  
Induced Defense ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Dependent Manner ◽  
Plant Host

AbstractThe success of Bacillus amyloliquefaciens as a biological control agent relies on its ability to outgrow plant pathogens. It is also thought to interact with its plant host by inducing systemic resistance. In this study, the ability of B. amyloliquefaciens MBI600 to elicit defense (or other) responses in tomato seedlings and plants was assessed upon the expression of marker genes and transcriptomic analysis. Spray application of Serifel, a commercial formulation of MBI600, induced responses in a dose-dependent manner. Low dosage primed plant defense by activation of SA-responsive genes. Suggested dosage induced defense by mediating synergistic cross-talk between JA/ET and SA-signaling. Saturation of tomato roots or leaves with MBI600 elicitors activated JA/ET signaling at the expense of SA-mediated responses. The complex signaling network that is implicated in MBI600-tomato seedling interactions was mapped. MBI600 and flg22 (a bacterial flagellin peptide) elicitors induced, in a similar manner, biotic and abiotic stress responses by the coordinated activation of genes involved in JA/ET biosynthesis as well as hormone and redox signaling. This is the first study to suggest the activation of plant defense following the application of a commercial microbial formulation under conditions of greenhouse crop production.

scholarly journals Characterization of Migration and Induced Resistance of Rhizobium Vitis Strain ARK-1, a Biological Control Agent Against Grapevine Crown Gall Disease

2020 ◽  
Author(s):  
Akira Kawaguchi ◽  
Yoshiteru Noutoshi
Keyword(s):  
Crown Gall ◽  
Temporal Dynamics ◽  
Biological Control Agent ◽  
Control Agent ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Cell Detection ◽  
Induced Expression ◽  
Crown Gall Disease ◽  
Grapevine Crown Gall

Abstract A nonpathogenic strain ARK-1 of Rhizobium vitis has an antagonistic activity toward tumorigenic (Ti) strain of R. vitis, a causal agent of grapevine crown gall disease, and works as a biocontrol agent. We have demonstrated that the gall formation was fully suppressed when ARK-1 was co-inoculated with Ti into the grapevine stem at a 1:1 ratio. For practical use of ARK-1 in agriculture, understanding the temporal dynamics of the bacterial habitat on host plants and the biocontrol property are needed in order to develop proper application methods. Here we demonstrated that the gall incidence by Ti was reduced to about 50% when ARK-1 was pre-inoculated at both upper and lower positions on the grapevine stem 3 cm away from the Ti-inoculation point 5 days before. The bacterial cell detection assay in the grapevine tissue revealed that ARK-1 could migrate at least 3 cm in 5 days. Inoculations of ARK-1 or Ti induced expression of marker genes for defense-related phytohormones such as salicylic acid, jasmonic acid, and ethylene in grapevine within 3 days but they were diminished by 6 days. Inoculation of Ti 5 days after ARK-1 pre-inoculation induced expression of the marker genes except for the LOX-9 gene in a basically similar way to those without the pre-inoculation, suggesting that ARK-1 did not induce typical acquired systemic resistance or induced systemic resistance in grapevine, while the transcript of LOX-9 was detected at 24 and 48 hours after the Ti inoculation when ARK-1 was pre-inoculated, unlike the un-inoculated condition. ARK-1 primed the induction of certain defense genes and it may take part in its biocontrol activity.

Interaction of a biological control agent, Chaetomium globosum, with seed coat microflora

1982 ◽  
Vol 28 (4) ◽  
pp. 431-437 ◽  
Author(s):  
J. P. Hubbard ◽  
G. E. Harman ◽  
C. J. Eckenrode
Keyword(s):  
Seed Coat ◽  
Plant Pathogens ◽  
Biological Control Agent ◽  
Control Agent ◽  
Selective Medium ◽  
Chaetomium Globosum ◽  
Bacterial Populations ◽  
Soilborne Plant Pathogens ◽  
Pea Seeds ◽  
Logarithmic Growth

The mechanism by which Chaetomium globosum, applied as ascospores to squash, snap bean, and pea seeds, reduces damage caused by larvae of the seed-corn maggot, Hylemya platura (Meigen), and soilborne plant pathogens was investigated. Chaetomium globosum ascospores germinate rapidly and cover the seed coat with a dense mat of mycelium soon after seeds are planted in soil. However, if seeds are not treated with C. globosum before planting, other organisms rapidly colonize the seed coat during germination. Seed flies oviposit near seeds in response to the growth of pseudomonads on the seed surface. Studies employing a selective medium indicate that Pseudomonas become the most prevalent genus occurring on the seed coat during seed germination. Treatment of seed with C. globosum suppresses the logarithmic growth of pseudomonads on the seed coat but affects neither bacterial populations in the soil surrounding the seed nor germination of Fusarium solani f. sp. pisi chlamydospores, either on the seed coat or in the soil surrounding the seed. A water-insoluble antibiotic was extracted from C. globosum treated seeds. After systemtic examination of other possibilities, it was concluded that this nondiffusable antibiotic substance produced by C. globosum suppresses pseudomonads responsible for stimulation of oviposition by seed flies as well as the soilborne plant pathogens.

scholarly journals Tea Tree Oil Induces Systemic Resistance against Fusarium wilt in Banana and Xanthomonas Infection in Tomato Plants

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1137
Author(s):  
Ronaldo J. D. Dalio ◽  
Heros J. Maximo ◽  
Rafaela Roma-Almeida ◽  
Janaína N. Barretta ◽  
Eric M. José ◽  
...  
Keyword(s):  
Fusarium Wilt ◽  
Priming Effect ◽  
Xanthomonas Campestris ◽  
Plant Pathogens ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Tea Tree Oil ◽  
Tomato Plants ◽  
Resistance Induction ◽  
Tea Tree

The essential tea tree oil (TTO) derived from Melaleuca alternifolia plant is widely used as a biopesticide to protect crops from several plant-pathogens. Its activity raised queries regarding its ability to, not only act as a bio-fungicide or bio-bactericide, but also systemically inducing resistance in plants. This was examined by TTO application to banana plants challenged by Fusarium oxysporum f. sp. cubense (Foc, Race 1) causing Fusarium wilt and to tomato plants challenged by Xanthomonas campestris. Parameters to assess resistance induction included: disease development, enzymatic activity, defense genes expression correlated to systemic acquired resistance (SAR) and induced systemic resistance (ISR) and priming effect. Spraying TTO on field-grown banana plants infected with Foc and greenhouse tomato plants infected with Xanthomonas campestris led to resistance induction in both hosts. Several marker genes of salicylic acid, jasmonic acid and ethylene pathways were significantly up-regulated in parallel with symptoms reduction. For tomato plants, we have also recorded a priming effect following TTO treatment. In addition to fungicidal and bactericidal effect, TTO can be applied in more sustainable strategies to control diseases by enhancing the plants ability to defend themselves against pathogens and ultimately diminish chemical pesticides applications.

scholarly journals Molecular characteristics and spatial distribution of adult human corneal cell subtypes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ann J. Ligocki ◽  
Wen Fury ◽  
Christian Gutierrez ◽  
Christina Adler ◽  
Tao Yang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cross Sections ◽  
Cell Types ◽  
Marker Genes ◽  
Molecular Characteristics ◽  
Transcriptional Level ◽  
Human Cornea ◽  
Adult Human ◽  
And Migration

AbstractBulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.

There are no A1 and A2 astrocytes in brain

2021 ◽  
Author(s):  
Shuang-qi Gao
Keyword(s):  
Endothelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Sorting ◽  
Reactive Astrocytes ◽  
Marker Genes ◽  
Set Up ◽  
The Brain

Abstract Objectives The subsets of astrocytes in the brain have not been fully elucidated. Using bulk RNA sequencing, reactive astrocytes were divided into A1 versus A2. However, using single-cell RNAseq (ScRNAseq), astrocytes were divided into over two subsets. Our aim was to set up the correspondence between the fluorescent-activated cell sorting (FACS)-bulk RNAseq and ScRNAseq data. Results We found that most of reactive astrocytes (RAs) marker genes were expressed in endothelial cells but not in astrocytes, suggesting those marker genes are not suitable for astrocytic activation. The absence of A1 and A2 astrocytes in the brain.

scholarly journals Evaluation of single-cell classifiers for single-cell RNA sequencing data sets

2019 ◽  
Vol 21 (5) ◽  
pp. 1581-1595 ◽  
Author(s):  
Xinlei Zhao ◽  
Shuang Wu ◽  
Nan Fang ◽  
Xiao Sun ◽  
Jue Fan
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Reference Data ◽  
Predictive Accuracy ◽  
Cell Types ◽  
Superior Performance ◽  
Marker Genes ◽  
Data Sets ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing

Abstract Single-cell RNA sequencing (scRNA-seq) has been rapidly developing and widely applied in biological and medical research. Identification of cell types in scRNA-seq data sets is an essential step before in-depth investigations of their functional and pathological roles. However, the conventional workflow based on clustering and marker genes is not scalable for an increasingly large number of scRNA-seq data sets due to complicated procedures and manual annotation. Therefore, a number of tools have been developed recently to predict cell types in new data sets using reference data sets. These methods have not been generally adapted due to a lack of tool benchmarking and user guidance. In this article, we performed a comprehensive and impartial evaluation of nine classification software tools specifically designed for scRNA-seq data sets. Results showed that Seurat based on random forest, SingleR based on correlation analysis and CaSTLe based on XGBoost performed better than others. A simple ensemble voting of all tools can improve the predictive accuracy. Under nonideal situations, such as small-sized and class-imbalanced reference data sets, tools based on cluster-level similarities have superior performance. However, even with the function of assigning ‘unassigned’ labels, it is still challenging to catch novel cell types by solely using any of the single-cell classifiers. This article provides a guideline for researchers to select and apply suitable classification tools in their analysis workflows and sheds some lights on potential direction of future improvement on classification tools.

A pipeline for the genetic improvement of a biological control agent enhances its potential for controlling soil-borne plant pathogens

2021 ◽  
Vol 152 ◽  
pp. 104460
Author(s):  
Marcio Vinicius de Carvalho Barros Côrtes ◽  
Maythsulene Inacio de Sousa Oliveira ◽  
Jackeline Rossetti Mateus ◽  
Lucy Seldin ◽  
Valacia Lemes Silva-Lobo ◽  
...  
Keyword(s):  
Biological Control ◽  
Genetic Improvement ◽  
Plant Pathogens ◽  
Biological Control Agent ◽  
Control Agent

Rhodopseudomonas palustris quorum sensing molecule pC-HSL induces systemic resistance to TMV infection via up-regulation of NbSIPK/NbWIPK expressions in Nicotiana benthamiana

2020 ◽  
Author(s):  
Xiaohua Du ◽  
Renyan Huang ◽  
Zhuo Zhang ◽  
Deyong Zhang ◽  
Ju`e Cheng ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Nicotiana Benthamiana ◽  
Biological Activities ◽  
Plant Immunity ◽  
Rhodopseudomonas Palustris ◽  
Photosynthetic Bacterium ◽  
Homoserine Lactone ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Ros Scavenging

G-negative bacteria produce a myriad of N-acyl-homoserine lactones (AHLs) that can function as quorum sensing (QS) signaling molecules. AHLs are also known to regulate various plant biological activities. p-Coumaroyl-homoserine lactone (pC-HSL) is the only QS molecule produced by a photosynthetic bacterium, Rhodopseudomonas palustris (R. palustris). The role of pC-HSL in the interaction between R. palustris and plant has not been investigated. In this study, we investigated the effect of pC-HSL on plant immunity and have found that this QS molecule can induce a systemic resistance to Tobacco mosaic virus (TMV) infection in Nicotiana benthamiana (N. benthamiana). The results show that pC-HSL treatment can prolong the activation of two mitogen-associated protein kinase (MAPK) genes (i.e., NbSIPK and NbWIPK) and enhance the expression of transcription factor WRKY8 as well as immune response marker genes NbPR1 and NbPR10, leading to an increased accumulation of reactive oxygen species (ROS) in the TMV infected plants. Our results also show that pC-HSL treatment can increase activities of two ROS-scavenging enzymes, POD and SOD. Knockdown of NbSIPK or NbWIPK expression in N. benthamiana plants through VIGS nullified or attenuated pC-HSL-induced systemic resistance, indicating that the functioning of pC-HSL relies on the activity of those two kinases. Meanwhile, pC-HSL pre-treated plants also showed a strong induction of kinase activities of NbSIPK and NbWIPK post TMV inoculation. Taken together, our results demonstrate that pC-HSL treatment results in enhanced plant resistance to TMV infection, which is helpful to uncover the outcome of interaction between R. palustris and its host plants.

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