scholarly journals Metabolome and Transcriptome Analysis of the Response Mechanisms of Ginseng to Rust Root Symptoms

2021 ◽  
Author(s):  
Xingbo Bian ◽  
Yan Zhao ◽  
Shengyuan Xiao ◽  
He Yang ◽  
Yongzhong Han ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Plant Pathogen ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Vital Role ◽  
Mechanism Model ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction

Abstract Background: Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. It leads to a severe decline in the quality of ginseng. Results: Compared with Healthy ginseng (HG), 949 metabolites and 9451 genes in diseased tissues were significantly changed at the metabolic and transcription levels. The metabolic patterns of the diseased tissues changed significantly, and organic acids, alkaloids, alcohols, and phenols may play a vital role in the response of ginseng to this disease. There were significant differences in the expression of plant hormone signal transduction, phenylpropanoid biosynthesis, peroxidase pathway, and multiple genes in the plant-pathogen interaction pathway.Conclusion: The current study performed a comparative metabolome and transcriptome analysis of GRS and HG. Based on the findings at the transcriptional and metabolic levels, the mechanism model of ginseng response to rusty root symptoms was established. Our results provide new insights into ginseng's response to rusty root symptoms, which will help reveal the potential molecular mechanisms of this disease in ginseng.

scholarly journals Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingbo Bian ◽  
Yan Zhao ◽  
Shengyuan Xiao ◽  
He Yang ◽  
Yongzhong Han ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Soil Microbiology ◽  
Mechanism Model ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction ◽  
Molecular Profiles

Abstract Background Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with soil environmental degradation, which may involve changes in soil microbiology and physicochemical properties. Results In this study, GRS and healthy ginseng (HG) samples were used as experimental materials for comparative analysis of transcriptome and metabolome. Compared with those in HG samples, 949 metabolites and 9451 genes were significantly changed at the metabolic and transcriptional levels in diseased samples. The diseased tissues’ metabolic patterns changed, and the accumulation of various organic acids, alkaloids, alcohols and phenols in diseased tissues increased significantly. There were significant differences in the expression of genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the peroxidase pathway, and the plant-pathogen interaction pathway. Conclusion The current study involved a comparative metabolome and transcriptome analysis of GRS and HG samples. Based on the findings at the transcriptional and metabolic levels, a mechanism model of the ginseng response to GRS was established. Our results provide new insights into ginseng’s response to GRS, which will reveal the potential molecular mechanisms of this disease in ginseng.

scholarly journals Integrative analysis of transcriptome and proteome revealed nectary and nectar traits in the plant-pollinator interaction of Nitraria tangutorum Bobrov

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tingting Chen ◽  
Yanwei Zhou ◽  
Jingbo Zhang ◽  
Ye Peng ◽  
Xiuyan Yang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Differentially Expressed Genes ◽  
Plant Pathogen ◽  
Plant Hormone ◽  
Flavonoid Biosynthesis ◽  
Epidermal Cells ◽  
Differentially Expressed ◽  
Ascorbate Oxidase ◽  
Nitraria Tangutorum ◽  
Plant Pathogen Interaction

Abstract Background Nitraria tangutorum is an important desert shrub that shows resistance to drought, salt and wind erosion stresses. It is a central ecological species in its area. Here, we have studied how N. tangutorum has adapted to achieve a successful reproduction strategy. Results We found that N. tangutorum is mainly pollinated by insects of the Hymenoptera, Diptera and Coleoptera orders. Nitraria tangutorum has very small flowers, with the nectary composed of secretive epidermal cells from which nectar is secreted, located within the inner petals. In addition, analyzing the transcriptome of four successive flower developmental stages revealed that mainly differentially expressed genes associated with flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction show dynamic expression. From the nectar, we could identify seven important proteins, of which the L-ascorbate oxidase protein was first found in plant nectar. Based on the physiological functions of these proteins, we predict that floral nectar proteins of N. tangutorum play an important role in defending against microbial infestation and scavenging active oxygen. Conclusions This study revealed that N. tangutorum is an insect-pollinated plant and its nectary is composed of secretive epidermal cells that specialized into secretive trichomes. We identified a large number of differentially expressed genes controlling flower and nectary development, nectar biosynthesis and secretion, flavonoid biosynthesis, plant hormone signal transduction and plant-pathogen interaction. We suggest that proteins present in N. tangutorum nectar may have both an antibacterial and oxygen scavenging effect. These results provide a scientific basis for exploring how the reproductive system of N. tangutorum and other arid-desert plants functions.

Antennal transcriptome analysis and candidate olfactory genes in Crematogaster rogenhoferi

2021 ◽  
pp. 1-12
Author(s):  
Xiang Zhou ◽  
Jixing Guo ◽  
Mingxia Zhang ◽  
Chunxiu Bai ◽  
Zheng Wang ◽  
...  
Keyword(s):  
Biological Control ◽  
Transcriptome Analysis ◽  
Molecular Basis ◽  
Molecular Mechanisms ◽  
Biological Control Agent ◽  
Control Agent ◽  
Vital Role ◽  
Neuron Membrane ◽  
Ionotropic Receptors ◽  
Soft Scale

Abstract Crematogaster rogenhoferi (Hymenoptera: Formicidae), an omnivorous ant, is one of the dominant predatory natural enemies of a soft scale pest, Parasaissetia nigra Nietner (Homoptera: Coccidae), and can effectively control P. nigra populations in rubber forests. Olfaction plays a vital role in the process of predation. However, the information about the molecular mechanism of olfaction-evoked behaviour in C. rogenhoferi is limited. In this study, we conducted antennal transcriptome analysis to identify candidate olfactory genes. We obtained 53,892 unigenes, 16,185 of which were annotated. Based on annotations, we identified 49 unigenes related to chemoreception, including four odourant-binding proteins, three chemosensory proteins, 37 odourant receptors, two odourant ionotropic receptors and three sensory neuron membrane proteins. This is the first report on the molecular basis of the chemosensory system of C. rogenhoferi. The findings provide a basis for elucidating the molecular mechanisms of the olfactory-related behaviours of C. rogenhoferi, which would facilitate a better application of C. rogenhoferi as a biological control agent.

scholarly journals Transcriptome-Based Analysis of Phosphite-Induced Resistance against Pathogens in Rice

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1334
Author(s):  
Yuqing Huang ◽  
Shengguan Cai ◽  
Guoping Zhang ◽  
Songlin Ruan
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanism ◽  
Differentially Expressed Genes ◽  
Induced Resistance ◽  
Plant Hormone ◽  
Xanthomonas Oryzae ◽  
Pyricularia Grisea ◽  
Protection Effect ◽  
Phenylpropanoid Biosynthesis ◽  
Xanthomonas Oryzae Pv.Oryzae

Phosphite (PHI) has been used in the management of Phytophthora diseases since the 1970s.We assessed the effect of PHI on controlling the incidence of Xanthomonas oryzae pv.oryzae and Pyricularia grisea. As a result, PHI application significantly inhibited the incidence of the diseases. To clarify the molecular mechanism underlying this, a transcriptome study was employed. In total, 2064 differentially expressed genes (DEGs) were identified between control and PHI treatment. The key DEGs could be classified into phenylpropanoid biosynthesis (ko00940), starch and sucrose metabolism (ko00500), and plant hormone signal transduction (ko04075). The expressions of defense-related genes had a higher expression lever upon PHI treatment. This study provides new insights into the mechanism of protection effect of PHI against pathogens.

scholarly journals Transcriptome Analysis of Watermelon Leaves Reveals Candidate Genes Responsive to Cucumber green mottle mosaic virus Infection

2019 ◽  
Vol 20 (3) ◽  
pp. 610 ◽  
Author(s):  
Yuyan Sun ◽  
Min Fan ◽  
Yanjun He
Keyword(s):  
Mosaic Virus ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Pcr Analysis ◽  
Whole Plant ◽  
Plant Pathogen Interactions ◽  
Differently Expressed Genes

Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, which cause diseases in cucurbits, especially watermelon. In watermelon, symptoms develop on the whole plant, including leaves, stems, peduncles, and fruit. To better understand the molecular mechanisms of watermelon early responses to CGMMV infection, a comparative transcriptome analysis of 24 h CGMMV-infected and mock-inoculated watermelon leaves was performed. A total of 1641 differently expressed genes (DEGs) were identified, with 886 DEGs upregulated and 755 DEGs downregulated after CGMMV infection. A functional analysis indicated that the DEGs were involved in photosynthesis, plant–pathogen interactions, secondary metabolism, and plant hormone signal transduction. In addition, a few transcription factor families, including WRKY, MYB, HLH, bZIP and NAC, were responsive to the CGMMV-induced stress. To confirm the high-throughput sequencing results, 15 DEGs were validated by qRT-PCR analysis. The results provide insights into the identification of candidate genes or pathways involved in the responses of watermelon leaves to CGMMV infection.

scholarly journals Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Pibiao Shi ◽  
Minfeng Gu
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Plant Hormone ◽  
Stress Factors ◽  
Soil Conditions ◽  
Regulation Mechanism

Abstract Background Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. Results The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

Regulation of hemidesmosome dynamics and cell signaling by integrin α6β4

2021 ◽  
Vol 134 (18) ◽  
Author(s):  
Lisa te Molder ◽  
Jose M. de Pereda ◽  
Arnoud Sonnenberg
Keyword(s):  
Signal Transduction ◽  
Extracellular Matrix ◽  
Cell Adhesion ◽  
Epithelial Cells ◽  
Basement Membrane ◽  
Molecular Mechanisms ◽  
Vital Role ◽  
Cellular Processes ◽  
Integrin Α6β4

ABSTRACT Hemidesmosomes (HDs) are specialized multiprotein complexes that connect the keratin cytoskeleton of epithelial cells to the extracellular matrix (ECM). In the skin, these complexes provide stable adhesion of basal keratinocytes to the underlying basement membrane. Integrin α6β4 is a receptor for laminins and plays a vital role in mediating cell adhesion by initiating the assembly of HDs. In addition, α6β4 has been implicated in signal transduction events that regulate diverse cellular processes, including proliferation and survival. In this Review, we detail the role of α6β4 in HD assembly and beyond, and we discuss the molecular mechanisms that regulate its function.

scholarly journals Key Cannabis Salt-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Varieties

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2338
Author(s):  
Jiangjiang Zhang ◽  
Cuiping Zhang ◽  
Siqi Huang ◽  
Li Chang ◽  
Jianjun Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Mapk Signaling ◽  
Molecular Networks ◽  
Molecular Response ◽  
Rna Seq ◽  
Physiological Diversity ◽  
Phenylpropanoid Biosynthesis

For the dissection and identification of the molecular response mechanisms to salt stress in cannabis, an experiment was conducted surveying the diversity of physiological characteristics. RNA-seq profiling was carried out to identify differential expression genes and pathway which respond to salt stress in different cannabis materials. The result of physiological diversity analyses showed that it is more sensitive to proline contents in K94 than in W20; 6 h was needed to reach the maximum in K94, compared to 12 h in W20. For profiling 0–72 h after treatment, a total of 10,149 differentially expressed genes were identified, and 249 genes exhibited significantly diverse expression levels in K94, which were clustered in plant hormone signal transduction and the MAPK signaling pathway. A total of 371 genes showed significant diversity expression variations in W20, which were clustered in the phenylpropanoid biosynthesis and plant hormone signal transduction pathway. The pathway enrichment by genes which were identified in K94 and W20 showed a similar trend to those clustered in plant hormone signal transduction pathways and MAPK signaling. Otherwise, there were 85 genes which identified overlaps between the two materials, indicating that these may be underlying genes related to salt stress in cannabis. The 86.67% agreement of the RNA-seq and qRT-PCR indicated the accuracy and reliability of the RNA-seq technique. Additionally, the result of physiological diversity was consistent with the predicted RNA-seq-based findings. This research may offer new insights into the molecular networks mediating cannabis to respond to salt stress.

scholarly journals Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

2020 ◽  
Author(s):  
Pibiao Shi ◽  
Minfeng Gu
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Plant Hormone ◽  
Stress Factors ◽  
Soil Conditions ◽  
Regulation Mechanism

Abstract Background: Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.Results: The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. 117 DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions: We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

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