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

PeerJ ◽  
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.

scholarly journals 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

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.

scholarly journals 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

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.

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

2020 ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here, we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkali-tolerant genotype) and AM-314/MS-155 (alkali-sensitive genotype) under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: The alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress

2019 ◽  
Vol 12 (2) ◽  
pp. 55-66 ◽  
Author(s):  
Quandong Nong ◽  
Mingyong Zhang ◽  
Jiantong Chen ◽  
Mei Zhang ◽  
Huaping Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
De Novo Assembly ◽  
De Novo ◽  
Rna Seq ◽  
Hylocereus Polyrhizus

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals 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 ◽  
2019 ◽  
Vol 20 (1) ◽  
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.

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

2021 ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals Effects of Salt Stress on Photosynthetic Fluorescence Characteristics, Antioxidant System, and Osmoregulation of Coreopsis tinctoria Nutt.

HortScience ◽  
2021 ◽  
pp. 1-8
Author(s):  
Hong Jiang ◽  
Zhiyuan Li ◽  
Xiumei Jiang ◽  
Yong Qin
Keyword(s):  
Salt Stress ◽  
Soluble Protein ◽  
Enzyme System ◽  
Soluble Sugar ◽  
Soil Salinization ◽  
Salt Stress Tolerance ◽  
Fluorescence Parameters ◽  
Antioxidant Enzyme System ◽  
Coreopsis Tinctoria ◽  
Fluorescence Characteristics

Coreopsis tinctoria Nutt. (C. tinctoria) is used in composite tea material and has important medicinal functions. Soil salinization affects the growth and development of C. tinctoria in Xinjiang (China). Here, we discussed the changes in photosynthesis and physiological characteristics of C. tinctoria seedlings treated with different concentrations of NaCl [0 (CK), 50, 100, 150, 200, and 250 mmol·L−1] for 12, 24, and 72 hours. The results showed that the net photosynthetic rate (Pn), stomatal conductance (gS), transpiration rate (Tr), and stomatal inhibition rate (Ls) decreased significantly with increasing concentrations of NaCl. Salt stress promoted the accumulation of peroxidase (POD), catalase (CAT), soluble sugar, soluble protein, and free proline (Pro). A highly significant positive correlation was found between Ls and Fv/Fm; Ls and Fv/Fo; soluble sugar and CAT; soluble sugar and soluble protein. C. tinctoria was most sensitive to the concentrations of 150 to 250 mmol·L−1 NaCl, and its salt stress tolerance was increased by reducing photosynthetic fluorescence parameters, improving the antioxidant enzyme system, and regulating osmotic substances.

scholarly journals Raspberry ketone diet supplement reduces attraction of sterile male Queensland fruit fly to cuelure by altering expression of chemoreceptor genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammed Abul Monjur Khan ◽  
Nandan P. Deshpande ◽  
Lucas A. Shuttleworth ◽  
Terry Osborne ◽  
Damian Collins ◽  
...  
Keyword(s):  
De Novo ◽  
Fruit Fly ◽  
Synthetic Analogue ◽  
Adult Males ◽  
Sterile Male ◽  
Rna Seq ◽  
Altered Expression ◽  
Raspberry Ketone ◽  
Male Annihilation ◽  
Transcriptional Changes

AbstractSterile male Queensland fruit fly, Bactrocera tryoni (Froggatt), fed as immature adults on the plant compound raspberry ketone (RK), show a reduced attraction to cuelure, a synthetic analogue of RK used as an attractant in Male Annihilation Technique. We hypothesized the reduced attraction of RK-fed adult males to cuelure may be a consequence of altered expression of chemoreception genes. A Y-tube olfactometer assay with RK-fed and RK-unfed sterile B. tryoni males tested the subsequent behavioural response to cuelure. Behavioral assays confirmed a significant decrease in attraction of RK-fed sterile males to cuelure. RK-fed, non-responders (to cue-lure) and RK-unfed, responders (to cue-lure) males were sampled and gene expression compared by de novo RNA-seq analysis. A total of 269 genes in fly heads were differentially expressed between replicated groups of RK-fed, cuelure non-responders and RK-unfed, cuelure responders. Among them, 218 genes including 4 chemoreceptor genes were up regulated and 51 genes were down regulated in RK-fed, cuelure non-responders. De novo assembly generated many genes with unknown functions and no significant BLAST hits to homologues in other species. The enriched and suppressed genes reported here, shed light on the transcriptional changes that affect the dynamics of insect responses to chemical stimuli.

scholarly journals Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
John A Burns ◽  
Huanjia Zhang ◽  
Elizabeth Hill ◽  
Eunsoo Kim ◽  
Ryan Kerney
Keyword(s):  
Stress Responses ◽  
De Novo ◽  
Innate Immune ◽  
Rna Seq ◽  
Animal Cells ◽  
Algal Symbiosis ◽  
Transcriptional Changes ◽  
Algal Endosymbiont ◽  
Oophila Amblystomatis ◽  
Egg Capsule

During embryonic development, cells of the green alga Oophila amblystomatis enter cells of the salamander Ambystoma maculatum forming an endosymbiosis. Here, using de novo dual-RNA seq, we compared the host salamander cells that harbored intracellular algae to those without algae and the algae inside the animal cells to those in the egg capsule. This two-by-two-way analysis revealed that intracellular algae exhibit hallmarks of cellular stress and undergo a striking metabolic shift from oxidative metabolism to fermentation. Culturing experiments with the alga showed that host glutamine may be utilized by the algal endosymbiont as a primary nitrogen source. Transcriptional changes in salamander cells suggest an innate immune response to the alga, with potential attenuation of NF-κB, and metabolic alterations indicative of modulation of insulin sensitivity. In stark contrast to its algal endosymbiont, the salamander cells did not exhibit major stress responses, suggesting that the host cell experience is neutral or beneficial.

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