cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13013927
title: Plant defensin expression triggered by fungal pathogen invasion depends on EDR1 protein kinase and ORA59 transcription factor in <i>Arabidopsis thaliana</i>

description: <i>Arabidopsis thaliana</i> exhibits durable ‘non-host’ resistance against the hemibiotrophic fungal pathogen <i>Colletotrichum tropicale</i> that infects mulberry plants. <i>Arabidopsis</i> non-host resistance comprises two layers of defense: preinvasive and postinvasive resistance. The EDR1 protein kinase contributes to <i>Arabidopsis</i> preinvasive resistance against <i>C. tropicale</i> by inducing the expression of plant defensin (<i>PDF</i>) genes. Here we report that the expressions of multiple <i>PDF</i> genes were strongly induced in <i>Arabidopsis</i> upon invasion by <i>C. tropicale</i>. Invasion by a necrotrophic pathogen, <i>Alternaria brassicicola</i>, also induced <i>PDF</i> expression. Importantly, <i>PDF</i> expression triggered upon invasion by both pathogens was inhibited in <i>edr1</i> mutants, indicating the requirement of EDR1 for <i>PDF</i> expression in postinvasive resistance by <i>Arabidopsis</i>. Analysis of <i>ora59</i> mutants also revealed that this gene is critical for induced <i>PDF</i> expression following pathogen invasion. Furthermore, inoculation assays of <i>A. brassicicola</i> indicated that <i>ORA59</i> is involved in postinvasive resistance against the pathogen, suggesting invasion-triggered <i>PDF</i> expression contributes to postinvasive resistance in <i>Arabidopsis.</i>
DOI: 10.6084/m9.figshare.13013927.v1
title: Plant defensin expression triggered by fungal pathogen invasion depends on EDR1 protein kinase and ORA59 transcription factor in <i>Arabidopsis thaliana</i>

description: <i>Arabidopsis thaliana</i> exhibits durable ‘non-host’ resistance against the hemibiotrophic fungal pathogen <i>Colletotrichum tropicale</i> that infects mulberry plants. <i>Arabidopsis</i> non-host resistance comprises two layers of defense: preinvasive and postinvasive resistance. The EDR1 protein kinase contributes to <i>Arabidopsis</i> preinvasive resistance against <i>C. tropicale</i> by inducing the expression of plant defensin (<i>PDF</i>) genes. Here we report that the expressions of multiple <i>PDF</i> genes were strongly induced in <i>Arabidopsis</i> upon invasion by <i>C. tropicale</i>. Invasion by a necrotrophic pathogen, <i>Alternaria brassicicola</i>, also induced <i>PDF</i> expression. Importantly, <i>PDF</i> expression triggered upon invasion by both pathogens was inhibited in <i>edr1</i> mutants, indicating the requirement of EDR1 for <i>PDF</i> expression in postinvasive resistance by <i>Arabidopsis</i>. Analysis of <i>ora59</i> mutants also revealed that this gene is critical for induced <i>PDF</i> expression following pathogen invasion. Furthermore, inoculation assays of <i>A. brassicicola</i> indicated that <i>ORA59</i> is involved in postinvasive resistance against the pathogen, suggesting invasion-triggered <i>PDF</i> expression contributes to postinvasive resistance in <i>Arabidopsis.</i>
DOI: 10.6084/m9.figshare.12951226.v1
title: Data-mining bioinformatics: suggesting <i>Arabidopsis thaliana</i> L-type lectin receptor kinase IX.2 (<i>LecRK-IX.2</i>) modulate metabolites and abiotic stress responses

description: The central role of the Arabidopsis <i>LecRK-IX.2</i> gene in response to biotic stress has been well established by an array of workers. So far, the role of <i>LecRK-IX.2</i> in abiotic stresses has not been investigated systematically. Here, we have first investigated a comprehensive <i>in silico</i> survey to explore the regulation, expression pattern in responses to a wide range of abiotic stresses. The present study reveals that the <i>LecRK-IX.2</i> promoter has numerous potential <i>cis</i>-regulatory elements (CREs) that are regulated by different stresses. AtGenExpress data elucidate that <i>LecRK-IX.2</i> gene plays a potential role in responses to cold, osmotic, drought, salt, UV-B, heat, wound, and genotoxic compound. The expression profile of the co-expressed genes suggests that Arabidopsis <i>LecRK-IX.2</i> gene might have a potential role in stress responses in a tissue-specific manner. Furthermore, a probable signal transduction mechanism has been described by using protein–protein interaction (PPI) dataset. Moreover, the present data-mining investigations have suggested that <i>LecRK-IX.2</i> gene modulates cellular metabolites and abiotic stress responses.
DOI: 10.6084/m9.figshare.13491140
title: The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of <i>ALTERNATIVE OXIDASE1a</i> under high intensity light

description: We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and <i>AOX1a</i> transgenic <i>Arabidopsis thaliana</i> following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The <i>AOX1a</i> overexpressing line (XX-2) showed the highest amount of <i>AOX1a</i> transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6–8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed ‘overcompensation effects’ prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with <i>AOX1a</i>, light- and stress-related <i>cis</i>-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of <i>AOX1a</i> expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.
DOI: 10.6084/m9.figshare.12951226
title: Data-mining bioinformatics: suggesting <i>Arabidopsis thaliana</i> L-type lectin receptor kinase IX.2 (<i>LecRK-IX.2</i>) modulate metabolites and abiotic stress responses

description: The central role of the Arabidopsis <i>LecRK-IX.2</i> gene in response to biotic stress has been well established by an array of workers. So far, the role of <i>LecRK-IX.2</i> in abiotic stresses has not been investigated systematically. Here, we have first investigated a comprehensive <i>in silico</i> survey to explore the regulation, expression pattern in responses to a wide range of abiotic stresses. The present study reveals that the <i>LecRK-IX.2</i> promoter has numerous potential <i>cis</i>-regulatory elements (CREs) that are regulated by different stresses. AtGenExpress data elucidate that <i>LecRK-IX.2</i> gene plays a potential role in responses to cold, osmotic, drought, salt, UV-B, heat, wound, and genotoxic compound. The expression profile of the co-expressed genes suggests that Arabidopsis <i>LecRK-IX.2</i> gene might have a potential role in stress responses in a tissue-specific manner. Furthermore, a probable signal transduction mechanism has been described by using protein–protein interaction (PPI) dataset. Moreover, the present data-mining investigations have suggested that <i>LecRK-IX.2</i> gene modulates cellular metabolites and abiotic stress responses.
DOI: 10.6084/m9.figshare.12929038
title: Isolation and identification of beneficial orchid mycorrhizal fungi in <i>Bletilla striata</i> (Thunb.) Rchb.f.(Orchidaceae)

description: Orchid mycorrhizal fungi (OMF) are essential for orchids growth. <i>Bletilla striata</i> (Thunb.) Rchb.f.(Orchidaceae) has high ornamental and medicinal value. Beneficial OMF isolation is crucial to improve the survival rate of <i>B. striata</i> tissue culture and transplanting. In this study, we isolated and identified the beneficial OMF in <i>B. striata</i> from the roots of sterilized wild <i>B. striata</i> seedlings by culturing in four different mediums. The germination states of <i>B. striata</i> seeds inoculated with diverse OMF were classified and calculated. Fresh and dry weight increments of <i>B. striata</i> seedlings inoculated with diverse OMF were recorded after 90 d of culturing on 1/2 MS medium. ITS sequences of beneficial fungi were amplified by PCR and taxonomically identified using BLAST against the GenBank nucleotide database. Ten kinds of OMF strains were isolated from <i>B. striata</i> and named R1 to R10. R6 significantly promoted <i>B. striata</i> seeds germination (<i>p</i> B. striata seedlings (<i>p</i> Serendipita. R3 was identified as <i>Schizothecium fimbriatum</i> by 100% ITS identity. R6 and R3 were beneficial OMF in <i>B. striata.</i>
DOI: 10.6084/m9.figshare.12220619
title: Alteration of iron responsive gene expression in Arabidopsis glutaredoxin <i>S17</i> loss of function plants with or without iron stress

description: Iron (Fe) is a mineral nutrient and a metal cofactor essential for plants. Iron limitation can have detrimental effects on plant growth and development, while excess iron inside plant cells leads to oxidative damage. As a result, plants have evolved complex regulatory networks to respond to fluctuations in cellular iron concentrations. The mechanisms that regulate these responses however, are not fully understood. Heterologous expression of an <i>Arabidopsis thaliana</i> monothiol glutaredoxin S17 (GRXS17) suppresses the over-accumulation of iron in the <i>Saccharomyces cerevisiae</i> Grx3/Grx4 mutant and disruption of <i>GRXS17</i> causes plant sensitivity to exogenous oxidants and iron deficiency stress. GRXS17 may act as an important regulator in the plant’s ability to respond to iron deficiency stress and maintain redox homeostasis. Here, we extend this investigation by analyzing iron-responsive gene expression of the Fer-like iron deficiency-induced transcription factor (FIT) network (<i>FIT, IRT1, FRO1</i>, and <i>FRO2</i>) and the bHLH transcription factor POPEYE (PYE) network (<i>PYE, ZIF1, FRO3, NAS4</i>, and <i>BTS</i>) in <i>GRXS17</i> KO plants and wildtype controls grown under iron sufficiency and deficiency conditions. Our findings suggest that GRXS17 is required for tolerance to iron deficiency, and plays a negative regulatory role under conditions of iron sufficiency.
DOI: 10.6084/m9.figshare.12198603.v1
title: Comparative transcriptome analysis of differentially expressed genes between the fruit peel and flesh of the purple tomato cultivar ‘Indigo Rose’

description: Anthocyanins are considered health-promoting phytonutrients; however, anthocyanins strictly occurr in the fruit peel of purple tomato cultivars, making the total anthocyanin content limited per tomato fruit. In this study, we performed a transcriptome analysis between the fruit peel and flesh of a purple tomato cultivar ‘Indigo Rose’ at both the mature green stage and breaking stage. In total, 1,945 differently expressed genes, including 165 transcription factors, were detected between the fruit peel and flesh, both at and after the mature green stage. We further analyzed the transcription of anthocyanin biosynthesis genes and the regulatory genes composing the MYB-bHLH-WD40 (MBW) complex between the fruit peel and flesh at both development stages. In addition, several light-sensing genes and other transcription factor genes, including BBX family genes and WRKY genes, showed different expression patterns between the fruit peel and flesh. These findings deepen our understanding of anthocyanin biosynthesis in tomato fruit peels and facilitate the identification of genes limiting the anthocyanin biosynthesis in tomato fruit flesh.
DOI: 10.6084/m9.figshare.12929038.v1
title: Isolation and identification of beneficial orchid mycorrhizal fungi in <i>Bletilla striata</i> (Thunb.) Rchb.f.(Orchidaceae)

description: Orchid mycorrhizal fungi (OMF) are essential for orchids growth. <i>Bletilla striata</i> (Thunb.) Rchb.f.(Orchidaceae) has high ornamental and medicinal value. Beneficial OMF isolation is crucial to improve the survival rate of <i>B. striata</i> tissue culture and transplanting. In this study, we isolated and identified the beneficial OMF in <i>B. striata</i> from the roots of sterilized wild <i>B. striata</i> seedlings by culturing in four different mediums. The germination states of <i>B. striata</i> seeds inoculated with diverse OMF were classified and calculated. Fresh and dry weight increments of <i>B. striata</i> seedlings inoculated with diverse OMF were recorded after 90 d of culturing on 1/2 MS medium. ITS sequences of beneficial fungi were amplified by PCR and taxonomically identified using BLAST against the GenBank nucleotide database. Ten kinds of OMF strains were isolated from <i>B. striata</i> and named R1 to R10. R6 significantly promoted <i>B. striata</i> seeds germination (<i>p</i> B. striata seedlings (<i>p</i> Serendipita. R3 was identified as <i>Schizothecium fimbriatum</i> by 100% ITS identity. R6 and R3 were beneficial OMF in <i>B. striata.</i>
DOI: 10.6084/m9.figshare.12198603
title: Comparative transcriptome analysis of differentially expressed genes between the fruit peel and flesh of the purple tomato cultivar ‘Indigo Rose’

description: Anthocyanins are considered health-promoting phytonutrients; however, anthocyanins strictly occurr in the fruit peel of purple tomato cultivars, making the total anthocyanin content limited per tomato fruit. In this study, we performed a transcriptome analysis between the fruit peel and flesh of a purple tomato cultivar ‘Indigo Rose’ at both the mature green stage and breaking stage. In total, 1,945 differently expressed genes, including 165 transcription factors, were detected between the fruit peel and flesh, both at and after the mature green stage. We further analyzed the transcription of anthocyanin biosynthesis genes and the regulatory genes composing the MYB-bHLH-WD40 (MBW) complex between the fruit peel and flesh at both development stages. In addition, several light-sensing genes and other transcription factor genes, including BBX family genes and WRKY genes, showed different expression patterns between the fruit peel and flesh. These findings deepen our understanding of anthocyanin biosynthesis in tomato fruit peels and facilitate the identification of genes limiting the anthocyanin biosynthesis in tomato fruit flesh.
DOI: 10.6084/m9.figshare.12220619.v1
title: Alteration of iron responsive gene expression in Arabidopsis glutaredoxin <i>S17</i> loss of function plants with or without iron stress

description: Iron (Fe) is a mineral nutrient and a metal cofactor essential for plants. Iron limitation can have detrimental effects on plant growth and development, while excess iron inside plant cells leads to oxidative damage. As a result, plants have evolved complex regulatory networks to respond to fluctuations in cellular iron concentrations. The mechanisms that regulate these responses however, are not fully understood. Heterologous expression of an <i>Arabidopsis thaliana</i> monothiol glutaredoxin S17 (GRXS17) suppresses the over-accumulation of iron in the <i>Saccharomyces cerevisiae</i> Grx3/Grx4 mutant and disruption of <i>GRXS17</i> causes plant sensitivity to exogenous oxidants and iron deficiency stress. GRXS17 may act as an important regulator in the plant’s ability to respond to iron deficiency stress and maintain redox homeostasis. Here, we extend this investigation by analyzing iron-responsive gene expression of the Fer-like iron deficiency-induced transcription factor (FIT) network (<i>FIT, IRT1, FRO1</i>, and <i>FRO2</i>) and the bHLH transcription factor POPEYE (PYE) network (<i>PYE, ZIF1, FRO3, NAS4</i>, and <i>BTS</i>) in <i>GRXS17</i> KO plants and wildtype controls grown under iron sufficiency and deficiency conditions. Our findings suggest that GRXS17 is required for tolerance to iron deficiency, and plays a negative regulatory role under conditions of iron sufficiency.
DOI: 10.6084/m9.figshare.13376868
title: The Arabidopsis transcription factor NAI1 activates the <i>NAI2</i> promoter by binding to the G-box motifs

description: Brassicaceae plants, including <i>Arabidopsis thaliana</i>, develop endoplasmic reticulum (ER)-derived structures called ER bodies, which are involved in chemical defense against herbivores. NAI1 is a basic helix-loop-helix (bHLH) type transcription factor that regulates two downstream genes, <i>NAI2</i> and <i>BGLU23</i>, that are responsible for the ER body formation and function. Here, we examined the transcription factor function of NAI1, and found that NAI1 binds to the promoter region of <i>NAI2</i> and activates the <i>NAI2</i> promoter. The recombinant NAI1 protein recognizes the canonical and non-canonical G-box motifs in the <i>NAI2</i> promoter. Furthermore, we examined the DNA binding activity of NAI1 toward several E-box motifs in the <i>NAI2</i> and <i>BGLU23</i> promoters and found that NAI1 binds to a DNA fragment that includes an E-box motif from the <i>BGLU23</i> promoter. Subcellular localization of NAI1 was evident in the nucleus, which is consistent with its transcription factor function. Transient expression experiments in <i>Nicotiana benthamiana</i> leaves showed that GFP-NAI1 protein activated the <i>NAI2</i> promoter by binding to the two G-boxes of the promoter. Disruption of the G-boxes abolished the NAI1-dependent activation of the <i>NAI2</i> promoter. These results indicate that NAI1 has a DNA binding activity in a motif-dependent manner and suggest that NAI1 regulates <i>NAI2</i> and <i>BGLU23</i> gene expressions through binding to these DNA motifs in their promoters.
DOI: 10.6084/m9.figshare.13376868.v1
title: The Arabidopsis transcription factor NAI1 activates the <i>NAI2</i> promoter by binding to the G-box motifs

description: Brassicaceae plants, including <i>Arabidopsis thaliana</i>, develop endoplasmic reticulum (ER)-derived structures called ER bodies, which are involved in chemical defense against herbivores. NAI1 is a basic helix-loop-helix (bHLH) type transcription factor that regulates two downstream genes, <i>NAI2</i> and <i>BGLU23</i>, that are responsible for the ER body formation and function. Here, we examined the transcription factor function of NAI1, and found that NAI1 binds to the promoter region of <i>NAI2</i> and activates the <i>NAI2</i> promoter. The recombinant NAI1 protein recognizes the canonical and non-canonical G-box motifs in the <i>NAI2</i> promoter. Furthermore, we examined the DNA binding activity of NAI1 toward several E-box motifs in the <i>NAI2</i> and <i>BGLU23</i> promoters and found that NAI1 binds to a DNA fragment that includes an E-box motif from the <i>BGLU23</i> promoter. Subcellular localization of NAI1 was evident in the nucleus, which is consistent with its transcription factor function. Transient expression experiments in <i>Nicotiana benthamiana</i> leaves showed that GFP-NAI1 protein activated the <i>NAI2</i> promoter by binding to the two G-boxes of the promoter. Disruption of the G-boxes abolished the NAI1-dependent activation of the <i>NAI2</i> promoter. These results indicate that NAI1 has a DNA binding activity in a motif-dependent manner and suggest that NAI1 regulates <i>NAI2</i> and <i>BGLU23</i> gene expressions through binding to these DNA motifs in their promoters.
DOI: 10.6084/m9.figshare.13330296
title: Elevated production of reactive oxygen species is related to host plant resistance to sugarcane aphid in sorghum.

description: Sugarcane aphid (<i>Melanaphis sacchari)</i> is a phloem-feeding insect that severely affects the growth and productivity of sorghum and other related crops. While a growing body of knowledge is accumulating regarding plant, and insect interactions, the role of reactive oxygen species (ROS) against aphid infestation in sorghum has not been established yet. Here, the involvement of H<sub>2</sub>O<sub>2</sub> and ROS detoxification enzymes in host plant resistance to sugarcane aphid in sorghum was demonstrated. The H<sub>2</sub>O<sub>2</sub> accumulation and expression patterns of selected ROS scavenging enzymes including ascorbate peroxidase (<i>APX</i>), glutathione S transferase (<i>GST</i>), superoxide dismutase (<i>SOD</i>), and catalase (<i>CAT</i>) in response to sugarcane aphid infestation at 3, 6, 9, and 12 days post infestation (dpi) in resistant (Tx2783) and susceptible (Tx7000) sorghum genotypes were assessed, respectively. A significant increase in H<sub>2</sub>O<sub>2</sub> accumulation was observed in resistant genotypes at all time points studied as compared to susceptible plants. Furthermore, gene expression analysis revealed that in responding to attack by sugarcane aphid, antioxidant genes were induced in both genotypes, but much stronger in the resistant line. Furthermore, aphid survival and fecundity were significantly inhibited in resistant plants compared to susceptible plants. Taken together, our results suggest that the elevated accumulation of H<sub>2</sub>O<sub>2</sub> and the strong upregulation of the antioxidant genes in sorghum may have contributed to host plant resistance in Tx2783 against sugarcane aphid but the weak expression of those antioxidant genes in Tx7000 resulted in the failure of attempting defense against sugarcane aphid. This report also provides the experimental evidence for the role of ROS involvement in the early defensive response to an attack by sugarcane aphid in sorghum.
DOI: 10.6084/m9.figshare.13330296.v1
title: Elevated production of reactive oxygen species is related to host plant resistance to sugarcane aphid in sorghum.

description: Sugarcane aphid (<i>Melanaphis sacchari)</i> is a phloem-feeding insect that severely affects the growth and productivity of sorghum and other related crops. While a growing body of knowledge is accumulating regarding plant, and insect interactions, the role of reactive oxygen species (ROS) against aphid infestation in sorghum has not been established yet. Here, the involvement of H<sub>2</sub>O<sub>2</sub> and ROS detoxification enzymes in host plant resistance to sugarcane aphid in sorghum was demonstrated. The H<sub>2</sub>O<sub>2</sub> accumulation and expression patterns of selected ROS scavenging enzymes including ascorbate peroxidase (<i>APX</i>), glutathione S transferase (<i>GST</i>), superoxide dismutase (<i>SOD</i>), and catalase (<i>CAT</i>) in response to sugarcane aphid infestation at 3, 6, 9, and 12 days post infestation (dpi) in resistant (Tx2783) and susceptible (Tx7000) sorghum genotypes were assessed, respectively. A significant increase in H<sub>2</sub>O<sub>2</sub> accumulation was observed in resistant genotypes at all time points studied as compared to susceptible plants. Furthermore, gene expression analysis revealed that in responding to attack by sugarcane aphid, antioxidant genes were induced in both genotypes, but much stronger in the resistant line. Furthermore, aphid survival and fecundity were significantly inhibited in resistant plants compared to susceptible plants. Taken together, our results suggest that the elevated accumulation of H<sub>2</sub>O<sub>2</sub> and the strong upregulation of the antioxidant genes in sorghum may have contributed to host plant resistance in Tx2783 against sugarcane aphid but the weak expression of those antioxidant genes in Tx7000 resulted in the failure of attempting defense against sugarcane aphid. This report also provides the experimental evidence for the role of ROS involvement in the early defensive response to an attack by sugarcane aphid in sorghum.