Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

Statement of withdrawalThe authors have withdrawn version 1 of this manuscript because a draft manuscript, which was still in the early stages of preparation and required major revisions including the replacement of the source RNA-seq datasets, was erroneously submitted. The authors do not wish this version to be cited as reference for this study. We will post a revised manuscript in the future. If you have any questions, please contact the corresponding author.

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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/v3 ◽

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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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/v2 ◽

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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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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RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection

BMC Genomics ◽

10.1186/s12864-015-1666-2 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 33

Author(s):

Aymeric Goyer ◽

Launa Hamlin ◽

James M. Crosslin ◽

Alex Buchanan ◽

Jeff H. Chang

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Rna Seq ◽

Potato Varieties ◽

Early Stages

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RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes

Developmental Biology ◽

10.1016/j.ydbio.2012.05.030 ◽

2012 ◽

Vol 368 (1) ◽

pp. 4-17 ◽

Cited By ~ 30

Author(s):

Eric W. Brunskill ◽

S. Steven Potter

Keyword(s):

Rna Processing ◽

Rna Seq ◽

Novel Genes ◽

Early Stages

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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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RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response

BMC Genomics ◽

10.1186/1471-2164-14-676 ◽

2013 ◽

Vol 14 (1) ◽

pp. 676 ◽

Cited By ~ 45

Author(s):

Carolina M Rodrigues ◽

Alessandra A de Souza ◽

Marco A Takita ◽

Luciano T Kishi ◽

Marcos A Machado

Keyword(s):

Defense Response ◽

Xylella Fastidiosa ◽

Citrus Reticulata ◽

Rna Seq ◽

Early Stages

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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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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.

Download Full-text