Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

Abstract Background Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Results Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. Conclusions The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

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Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

BMC Genomics ◽

10.1186/s12864-019-6229-5 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Marco Tulio Solano-De la Cruz ◽

Jacel Adame-García ◽

Josefat Gregorio-Jorge ◽

Verónica Jiménez-Jacinto ◽

Leticia Vega-Alvarado ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Translational Regulation ◽

Transcriptome Assembly ◽

Transcriptional Level ◽

Post Inoculation ◽

Molecular Response ◽

Vanilla Planifolia ◽

Rna Seq ◽

Early Stages ◽

Transcriptional Changes

Abstract Background Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Results Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. Conclusions The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

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Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

10.21203/rs.2.12054/v1 ◽

2019 ◽

Author(s):

Marco Tulio Solano-De la Cruz ◽

Jacel Adame-García ◽

Josefat Gregorio-Jorge ◽

Verónica Jiménez-Jacinto ◽

Leticia Vega-Alvarado ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Translational Regulation ◽

Transcriptome Assembly ◽

Transcriptional Level ◽

Post Inoculation ◽

Molecular Response ◽

Vanilla Planifolia ◽

Rna Seq ◽

Early Stages ◽

Transcriptional Changes

Abstract Background Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Results Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. Conclusions The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

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Transcriptional Changes in Potato Sprouts upon Interaction with Rhizoctonia solani Indicate Pathogen-Induced Interference in the Defence Pathways of Potato

International Journal of Molecular Sciences ◽

10.3390/ijms22063094 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3094

Author(s):

Rita Zrenner ◽

Bart Verwaaijen ◽

Franziska Genzel ◽

Burkhardt Flemer ◽

Rita Grosch

Keyword(s):

Rhizoctonia Solani ◽

Rna Sequencing ◽

Control Strategies ◽

Transcriptional Response ◽

Black Scurf ◽

Post Inoculation ◽

Molecular Response ◽

Resistance Level ◽

Sequencing Experiment ◽

Transcriptional Changes

Rhizoctonia solani is the causer of black scurf disease on potatoes and is responsible for high economical losses in global agriculture. In order to increase the limited knowledge of the plants’ molecular response to this pathogen, we inoculated potatoes with R. solani AG3-PT isolate Ben3 and carried out RNA sequencing with total RNA extracted from potato sprouts at three and eight days post inoculation (dpi). In this dual RNA-sequencing experiment, the necrotrophic lifestyle of R. solani AG3-PT during early phases of interaction with its host has already been characterised. Here the potato plants’ comprehensive transcriptional response to inoculation with R. solani AG3 was evaluated for the first time based on significantly different expressed plant genes extracted with DESeq analysis. Overall, 1640 genes were differentially expressed, comparing control (−Rs) and with R. solani AG3-PT isolate Ben3 inoculated plants (+Rs). Genes involved in the production of anti-fungal proteins and secondary metabolites with antifungal properties were significantly up regulated upon inoculation with R. solani. Gene ontology (GO) terms involved in the regulation of hormone levels (i.e., ethylene (ET) and jasmonic acid (JA) at 3 dpi and salicylic acid (SA) and JA response pathways at 8 dpi) were significantly enriched. Contrastingly, the GO term “response to abiotic stimulus” was down regulated at both time points analysed. These results may support future breeding efforts toward the development of cultivars with higher resistance level to black scurf disease or the development of new control strategies.

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Increase in ribosomal proteins activity: Translational reprogramming in Vanilla planifolia Jacks., against Fusarium infection

10.1101/660860 ◽

2019 ◽

Cited By ~ 1

Author(s):

Marco Tulio Solano de la Cruz ◽

Jacel Adame-García ◽

Josefat Gregorio-Jorge ◽

Verónica Jiménez-Jacinto ◽

Leticia Vega-Alvarado ◽

...

Keyword(s):

Ribosomal Proteins ◽

Translational Regulation ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Global Gene Expression ◽

Early Response ◽

Defense Responses ◽

Transcriptional Level ◽

Vanilla Planifolia ◽

Transcriptional Reprogramming

ABSTRACTBackgroundUpon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptomical changes must occur during interactions with pathogens, this causing the triggering of pathogen- and plant-derived molecules. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae. This pathogen causes root and stem rot in vanilla plants that finally leads to plant death. To further investigate how vanilla plants respond at the transcriptional level upon infection with F.oxysporum f. sp. vanillae, we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection.ResultsAnalysis of global gene expression profiles indicated that a major transcriptional change occurs at 2 dpi, in comparison to 10 dpi, whereas 3420 genes were found with a differential expression at 2 dpi, only 839 were identified at 10 dpi. The analysis of the transcriptional profile at 2 dpi suggests that vanilla plants prepare to counter the infection by gathering a pool of translational regulation-related transcripts.ConclusionsWe propose that the plant-pathogen interaction at early stages causes a transcriptional reprogramming coupled with a translational regulation. Altogether, this study provides the identification of molecular players that could help to fight the most damaging disease of vanilla, where ribosomal proteins and regulation of the translational mechanism are critical. These are insights into the defense responses of V. planifolia Jacks., providing the basis for the understanding of the plant early response towards biotic stress.

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Metatranscriptomic comparison of endophytic and pathogenic Fusarium–Arabidopsis interactions reveals plant transcriptional plasticity

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-21-0063-r ◽

2021 ◽

Author(s):

Li Guo ◽

Houlin Yu ◽

Bo Wang ◽

Kathryn Vescio ◽

Gregory A. DeIulio ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Stress Responses ◽

Fungal Endophytes ◽

Plant Stress ◽

Fine Tuning ◽

Post Inoculation ◽

Molecular Response ◽

Plant Nitrogen ◽

Accessory Genes ◽

Transcriptional Plasticity

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (~80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.

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Metatranscriptomic comparison of endophytic and pathogenic Fusarium–Arabidopsis interactions reveals plant transcriptional plasticity

10.1101/2021.03.01.433437 ◽

2021 ◽

Author(s):

Li Guo ◽

Houlin Yu ◽

Bo Wang ◽

Kathryn Vescio ◽

Gregory A. DeIulio ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Stress Responses ◽

Fungal Endophytes ◽

Fine Tuning ◽

Transcriptional Networks ◽

Post Inoculation ◽

Molecular Response ◽

Plant Nitrogen ◽

Accessory Genes ◽

Transcriptional Plasticity

ABSTRACTPlants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (∼80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.One-sentence summaryMultiomics analysis reveals the regulatory plasticity of plants in response to beneficial and antagonistic microbes, resulting in distinct phenotypes and rewired transcriptional networks.

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Physiological changes and transcript identification in Coreopsis tinctoria Nutt. in early stages of salt stress

PeerJ ◽

10.7717/peerj.11888 ◽

2021 ◽

Vol 9 ◽

pp. e11888

Author(s):

Hong Jiang ◽

Zhiyuan Li ◽

Xiumei Jiang ◽

Yong Qin

Keyword(s):

Salt Stress ◽

De Novo ◽

Soluble Sugar ◽

Rna Seq ◽

Early Stages ◽

Coreopsis Tinctoria ◽

Transcriptional Changes ◽

Physiological Indexes ◽

Highly Correlated ◽

Transcript Identification

Coreopsis tinctoria Nutt. (C. tinctoria) is a special tea ingredient that adapts to certain salt stresses and shares the functions of chrysanthemum. With annual expansion of the cultivation area of C. tinctoria in Xinjiang (China), soil salinity may become a constraint for chrysanthemum cultivation. To investigate the response of C. tinctoria to salt stress, physiological and transcriptional changes in C. tinctoria in the early stages of low (50 mM NaCl) and high (200 mM NaCl) salt stress were analyzed and identified. The results showed that the contents of osmotic regulators (free proline, soluble sugar, and soluble protein) and antioxidant enzymes (catalase and peroxidase) under salt stress increased to various extents compared with those of the control (CK) within 72 h, and the increase was higher under 200 mM NaCl treatments. De novo RNA-seq was used to analyze changes in the transcripts under 50 and 200 mM NaCl treatments for up to 48 h. In total, 8,584, 3,760, 7,833, 19,341, 13,233, and 9,224 differentially expressed genes (DEGs) were detected under 12 h, 24 h, and 48 h for 50 and 200 mM NaCl treatments, respectively. Weighted correlation network analysis (WGCNA) was used to analyze the correlations between all DEGs and physiological indexes. We found that the coexpression modules blue2 and Lightskyblue4 highly correlated with osmotic regulators and CAT and identified 20 and 30 hub genes, respectively. The results provide useful data for the further study of salt tolerance in C. tinctoria.

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Integrated RNA-seq and sRNA-seq revealed differences in transcriptome between susceptible and resistant tomato responding to Fusarium oxysporum

10.1101/324574 ◽

2018 ◽

Author(s):

Min Zhao ◽

Hui-Min Ji ◽

Ying Gao ◽

Xin-Xin Cao ◽

Hui-Ying Mao ◽

...

Keyword(s):

Gene Expression ◽

Disease Resistance ◽

Fusarium Oxysporum ◽

Expression Patterns ◽

Critical Role ◽

Mirna Gene ◽

Initial Point ◽

Resistant Cultivar ◽

Post Inoculation ◽

Rna Seq

ABSTRACTTomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to unravel regulated genes and miRNAs in tomato infected by FOL. Differentially expressed (DE) protein coding gene and miRNA gene profiles upon inoculation with FOL were presented at twenty-four hours post-inoculation including four treatments. Total of more than 182.6 million and 132.2 million high quality clean reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was found in DE mRNAs between susceptible cultivar Moneymaker and resistant cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. Combining with qRT-PCR, five disease resistance genes, Solyc01g095630, Solyc03g059080, Solyc00g174340, Solyc11g071750 and Solyc05g050350, were verified to involved in the disease resistance in the resistant cultivar Motelle treated with FOL. Northern blot analysis further confirmed the results from sRNA-Seq and demonstrated that several miRNAs including Sly-miR477-5p, sly-miR167a, novel_mir_675, novel_mir_504 and novel_mir_762 conferred FOL infection. Our data resulted that pathogen resistant genes/miRNAs may play a critical role with the benefit of a coordinated machinery in prompting the response in prompting FOL response in tomato, which offered us with a future direction and surely help in generating models of mediated resistance responses with assessment of genomic gene expression patterns.

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Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit

10.1101/340018 ◽

2018 ◽

Author(s):

Peter A. McAtee ◽

Lara Brian ◽

Ben Curran ◽

Otto van der Linden ◽

Niels J. Nieuwenhuizen ◽

...

Keyword(s):

Gene Expression ◽

Pseudomonas Syringae ◽

Time Course ◽

Secretion System ◽

Nutrient Acquisition ◽

Post Inoculation ◽

Rna Seq ◽

Type Iii ◽

Early Stages ◽

Expression Of Genes

AbstractBackgroundPseudomonas syringae is a widespread bacterial species complex that includes a number of significant plant pathogens. Amongst these, P. syringae pv. actinidiae (Psa) initiated a worldwide pandemic in 2008 on cultivars of Actinidia chinensis var. chinensis. To gain information about the expression of genes involved in pathogenicity we have carried out transcriptome analysis of Psa during the early stages of kiwifruit infection.ResultsGene expression in Psa was investigated during the first five days after infection of kiwifruit plantlets, using RNA-seq. Principal component and heatmap analyses showed distinct phases of gene expression during the time course of infection. The first phase was an immediate transient peak of induction around three hours post inoculation (HPI) that included genes that code for a Type VI Secretion System and nutrient acquisition (particularly phosphate). This was followed by a significant commitment, between 3 and 24 HPI, to the induction of genes encoding the Type III Secretion System (T3SS) and Type III Secreted Effectors (T3SE). Expression of these genes collectively accounted for 6.3% of the bacterial transcriptome at this stage. There was considerable variation in the expression levels of individual T3SEs but all followed the same temporal expression pattern, with the exception of HopAS1, which peaked later in expression at 48 HPI. As infection progressed over the time course of five days, there was an increase in the expression of genes with roles in sugar, amino acid and sulfur transport and the production of alginate and colanic acid. These are both polymers that are major constituents of extracellular polysaccharide substances (EPS) and are involved in biofilm production. Reverse transcription-quantitative PCR (RT-qPCR) on an independent infection time course experiment showed that the expression profile of selected bacterial genes at each infection phase correlated well with the RNA-seq data.ConclusionsThe results from this study indicate that there is a complex remodeling of the transcriptome during the early stages of infection, with at least three distinct phases of coordinated gene expression. These include genes induced during the immediate contact with the host, those involved in the initiation of infection, and finally those responsible for nutrient acquisition.

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