scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

Identification of saponins detoxification genes in I. mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

Abstract Saponins are kinds of antifungal compounds produced by P. notoginseng to resist invasion by pathogens. I. mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4 H and 12 H compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4 H and 12 H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation-reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen-Host Interaction) genes out of those 93 up-regulated genes. In this report, we identified virulence associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 362 ◽  
Author(s):  
Monise Petrucelli ◽  
Kamila Peronni ◽  
Pablo Sanches ◽  
Tatiana Komoto ◽  
Josie Matsuda ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Trichophyton Rubrum ◽  
Glyoxylate Cycle ◽  
Human Keratinocytes ◽  
Rna Seq ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding ◽  
Hacat Keratinocyte

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum–host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

scholarly journals Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis

2019 ◽  
Author(s):  
Adela Zumaquero ◽  
Satoko Kanematsu ◽  
Hitoshi Nakayashiki ◽  
Antonio Matas ◽  
Elsa Martínez-Ferri ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Root Rot ◽  
Molecular Mechanisms ◽  
Plant Cell Wall ◽  
Infection Process ◽  
Rosellinia Necatrix ◽  
White Root Rot ◽  
Root Rot Disease ◽  
Host Interaction ◽  
Rot Disease

Abstract Background White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado `Dusa´ roots with that obtained from the fungus cultured in rich medium. Results The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1,937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction. Conclusions The analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.

scholarly journals Gene Expression Response ofTrichophyton rubrumduring Coculture on Keratinocytes Exposed to Antifungal Agents

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Tatiana Takahasi Komoto ◽  
Tamires Aparecida Bitencourt ◽  
Gabriel Silva ◽  
Rene Oliveira Beleboni ◽  
Mozart Marins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Citrate Synthase ◽  
Isocitrate Lyase ◽  
Glyoxylate Cycle ◽  
Serine Proteinase ◽  
Gene Expression Response ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding

Trichophyton rubrumis the most common causative agent of dermatomycoses worldwide, causing infection in the stratum corneum, nails, and hair. Despite the high prevalence of these infections, little is known about the molecular mechanisms involved in the fungal-host interaction, particularly during antifungal treatment. The aim of this work was to evaluate the gene expression ofT. rubrumcocultured with keratinocytes and treated with the flavonoidtrans-chalcone and the glycoalkaloidα-solanine. Both substances showed a marked antifungal activity againstT. rubrumstrain CBS (MIC = 1.15 and 17.8 µg/mL, resp.). Cytotoxicity assay against HaCaT cells produced IC50values of 44.18 totrans-chalcone and 61.60 µM toα-solanine. The interaction of keratinocytes withT. rubrumconidia upregulated the expression of genes involved in the glyoxylate cycle, ergosterol synthesis, and genes encoding proteases but downregulated the ABC transporterTruMDR2 gene. However, both antifungals downregulated the ERG1 and ERG11, metalloprotease 4, serine proteinase, andTruMDR2 genes. Furthermore, thetrans-chalcone downregulated the genes involved in the glyoxylate pathway, isocitrate lyase, and citrate synthase. Considering the urgent need for more efficient and safer antifungals, these results contribute to a better understanding of fungal-host interactions and to the discovery of new antifungal targets.

scholarly journals Genomic and Transcriptomic Analysis Provide Insights Into Root Rot Resistance in Panax notoginseng

2021 ◽  
Vol 12 ◽  
Author(s):  
Kang Ning ◽  
Mengzhi Li ◽  
Guangfei Wei ◽  
Yuxin Zhou ◽  
Guozhuang Zhang ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Defense Response ◽  
Root Rot ◽  
Panax Notoginseng ◽  
Rna Seq ◽  
Resistant Genotype ◽  
Hub Gene ◽  
Medicinal Value ◽  
Resistant Varieties ◽  
Plant Pathogen Interaction

Panax notoginseng (Panax notoginseng (Burk.) F.H. Chen), a plant of high medicinal value, is severely affected by root rot during cultivation. Here, we generated a reference genome of P. notoginseng, with a contig N50 size of 241.268 kb, and identified 66 disease-resistance genes (R-genes) as candidate genes for breeding disease-resistant varieties. We then investigated the molecular mechanism underlying the responses of resistant and susceptible P. notoginseng genotypes to Fusarium oxysporum infection at six time points by RNA-seq. Functional analysis of the genes differentially expressed between the two genotypes indicated that genes involved in the defense response biological process like hormone transduction and plant-pathogen interaction are continuously and highly expressed in resistant genotype during infection. Moreover, salicylic acid and jasmonic acid levels gradually increased during infection in the resistant genotype. Coexpression analysis showed that PnWRKY22 acts as a hub gene in the defense response of the resistant genotype. Finally, transiently overexpressing PnWRKY22 increased salicylic acid levels in P. notoginseng leaves. Our findings provide a theoretical basis for studying root rot resistance in P. notoginseng.

scholarly journals Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Wei Wang ◽  
Yi Dai ◽  
Mingchun Wang ◽  
Wenpeng Yang ◽  
Degang Zhao
Keyword(s):  
Molecular Mechanisms ◽  
Degradation Pathway ◽  
Endosperm Development ◽  
Rna Seq ◽  
Wild Type ◽  
Genes Encoding ◽  
Recessive Mutant ◽  
Lysine Degradation ◽  
Tryptophan Content

In maize, pyramiding of o2 and o16 alleles can greatly improve the nutritional quality of grains. To dissect its molecular mechanism, we created a double recessive mutant line, o2o2o16o16, by introgression of the o2 and o16 alleles into the wild-type maize inbred line, by molecular marker-assisted backcross selection. The kernels (18 day after pollination (DAP), 28 DAP, and 38 DAP) of the o2o2o16o16 mutant and its parent lines were subject to RNA sequencing (RNA-Seq). The RNA-Seq analysis revealed that 59 differentially expressed genes (DEGs) were involved in lysine metabolism and 43 DEGs were involved in tryptophan metabolism. Among them, the genes encoding AK, ASADH, and Dap-F in the lysine synthesis pathway were upregulated at different stages of endosperm development, promoting the synthesis of lysine. Meanwhile, the genes encoding LKR/SDH and L-PO in the lysine degradation pathway were downregulated, inhibiting the degradation of lysine. Moreover, the genes encoding TAA and YUC in the tryptophan metabolic pathway were downregulated, restraining the degradation of tryptophan. Thus, pyramiding o2 and o16 alleles could increase the lysine and tryptophan content in maize. These above results would help to uncover the molecular mechanisms involved in the increase in lysine and the tryptophan content, through the introgression of o2 and o16 alleles into the wild-type maize.

scholarly journals Discovery of GLO1 New Related Genes and Pathways by RNA-Seq on A2E-Stressed Retinal Epithelial Cells Could Improve Knowledge on Retinitis Pigmentosa

Antioxidants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 416 ◽  
Author(s):  
Luigi Donato ◽  
Concetta Scimone ◽  
Simona Alibrandi ◽  
Giacomo Nicocia ◽  
Carmela Rinaldi ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Retinitis Pigmentosa ◽  
Molecular Mechanisms ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Retrograde Transport ◽  
Antioxidant Systems ◽  
Rna Seq ◽  
Starting Point ◽  
Significant Expression

Endogenous antioxidants protect cells from reactive oxygen species (ROS)-related deleterious effects, and an imbalance in the oxidant/antioxidant systems generates oxidative stress. Glyoxalase 1 (GLO1) is a ubiquitous cellular enzyme involved in detoxification of methylglyoxal (MG), a cytotoxic byproduct of glycolysis whose excess can produce oxidative stress. In retinitis pigmentosa, one of the most diffuse cause of blindness, oxidative damage leads to photoreceptor death. To clarify the role of GLO1 in retinitis pigmentosa onset and progression, we treated human retinal pigment epithelium cells by the oxidant agent A2E. Transcriptome profiles between treated and untreated cells were performed by RNA-Seq, considering two time points (3 and 6 h), after the basal one. The exposure to A2E highlighted significant expression differences and splicing events in 370 GLO1 first-neighbor genes, and 23 of them emerged from pathway clustered analysis as main candidates to be associated with retinitis pigmentosa. Such a hypothesis was corroborated by the involvement of previously analyzed genes in specific cellular activities related to oxidative stress, such as glyoxylate and dicarboxylate metabolism, glycolysis, axo-dendritic transport, lipoprotein activity and metabolism, SUMOylation and retrograde transport at the trans-Golgi network. Our findings could be the starting point to explore unclear molecular mechanisms involved in retinitis pigmentosa etiopathogenesis.

scholarly journals Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
A. Zumaquero ◽  
S. Kanematsu ◽  
H. Nakayashiki ◽  
A. Matas ◽  
E. Martínez-Ferri ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Root Rot ◽  
Molecular Mechanisms ◽  
Plant Cell Wall ◽  
Infection Process ◽  
Rosellinia Necatrix ◽  
White Root Rot ◽  
Root Rot Disease ◽  
Host Interaction ◽  
Rot Disease

Abstract Background White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado ‘Dusa’ roots with that obtained from the fungus cultured in rich medium. Results The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction. Conclusions The analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.

scholarly journals Transcriptome Analysis of the Grape-Elsinoë ampelina Pathosystem Reveals Novel Effectors and a Robust Defense Response

2020 ◽  
pp. MPMI-08-20-0227
Author(s):  
Zhi Li ◽  
Ya Wang ◽  
Yanchun Fan ◽  
Bilal Ahmad ◽  
Xianhang Wang ◽  
...  
Keyword(s):  
Host Response ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Carbohydrate Active Enzymes ◽  
Defense Systems ◽  
Host Interaction ◽  
Elsinoe Ampelina ◽  
Metabolite Synthesis ◽  
Fungal Genes ◽  
Open Access Article

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. In this study, a dual RNA-seq analysis was used to simultaneously monitor the fungal genes related to pathogenesis and grape genes related to defense during the interaction at 2, 3, 4, and 5 days postinoculation. Consistent with their potential roles in pathogenicity, genes for carbohydrate-active enzymes, secondary metabolite synthesis, pathogen-host interaction, and those encoding secreted proteins are upregulated during infection. Based on Agrobacterium tumefaciens–mediated transient assays in Nicotiana benthamiana, we further showed that eight and nine candidate effectors, respectively, suppressed BAX- and INF1-mediated programmed cell death. The host response was characterized by the induction of multiple defense systems against E. ampelina, including synthesis of phenylpropanoids, stilbenes, and terpenoid biosynthesis, cell-wall modifications, regulation by phytohormones, and expression of defense-related genes. Together, these findings offer new insights into molecular mechanisms underlying the grape–E. ampelina interaction. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1335
Author(s):  
Hsueh-Yuan Chang ◽  
Cindy B. S. Tong
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Phenotypic Differences ◽  
Genes Encoding ◽  
A Cell ◽  
Phenotypic Groups

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

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