cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19517985.v1
title: GIGANTEA regulates <i>PAD4</i> transcription to promote pathogen defense against <i>Hyaloperonospora arabidopsidis</i> in <i>Arabidopsis thaliana</i>

description: Plants have evolved a network of complex signaling pathways that allow them to cope with the fluctuations of internal and external environmental cues. GIGANTEA (GI), a well-known, highly conserved plant nuclear protein, has been shown to regulate multiple biological functions in plants such as circadian rhythm, light signaling, cold tolerance, hormone signaling, and photoperiodic flowering. Recently, the role of GI in disease tolerance against different pathogens has come to light; however, a detailed mechanism to understand the role of GI in pathogen defense remains largely unexplained. Here, we report that <i>GIGANTEA</i> is upregulated upon infection with a virulent oomycete pathogen, <i>Hyaloperonospora arabidopsidis</i> (<i>Hpa</i>), in <i>Arabidopsis thaliana</i> accession Col-0. To investigate the role of GI in <i>Arabidopsis</i> defense, we examined the pathogen infection phenotype of <i>gi</i> mutant plants and found that <i>gi-100</i> mutant was highly susceptible to <i>Hpa</i> Noco2 infection. Notably, the quantitative real-time PCR showed that <i>PHYTOALEXIN DEFICIENT4</i> (<i>PAD4</i>) and several PAD4-regulated downstream genes were downregulated upon Noco2 infection in <i>gi-100</i> mutant as compared to Col-0 plants. Furthermore, the chromatin immunoprecipitation results show that GI can directly bind to the intronic region of the <i>PAD4</i> gene, which might explain the mechanism of GI function in regulating disease resistance in plants. Taken together, our results suggest that <i>GI</i> expression is induced upon <i>Hpa</i> pathogen infection and GI can regulate the expression of <i>PAD4</i> to promote resistance against the oomycete pathogen <i>Hyaloperonospora arabidopsidis</i> in <i>Arabidopsis thaliana</i>.
DOI: 10.6084/m9.figshare.21587721
title: A glutamate receptor-like gene is involved in ABA-mediated growth control in <i>Physcomitrium</i> (<i>Physcomitrella) patens</i>

description: Plant glutamate receptor homologs (GLRs), which function as key calcium channels, play pivotal roles in various developmental processes as well as stress responses. The moss <i>Physcomitrium patens</i>, a representative of the earliest land plant lineage, possess multiple pathways of hormone signaling for coordinating growth and adaptation responses. However, it is not clear whether GLRs are connected to hormone-mediated growth control in the moss. In this study, we report that one of the two GLRs in <i>P. patens</i>, PpGLR1, involves in abscisic acid (ABA)-mediated growth regulation. ABA represses the growth of wild-type moss, and intriguingly, the <i>PpGLR1</i> transcript levels are significantly increased in response to ABA treatment, based on both gene expression and the <i>PpGLR1pro::GUS</i> reporter results. Furthermore, the growth of <i>Ppglr1</i> knockout moss mutants is hypersensitive to ABA treatment. These results suggest that PpGLR1 plays a critical role in ABA-mediated growth regulation, which provide useful information for our further investigation of the regulatory mechanism between Ca<sup>2+</sup> signal and ABA in moss growth control.
DOI: 10.6084/m9.figshare.21587721.v1
title: A glutamate receptor-like gene is involved in ABA-mediated growth control in <i>Physcomitrium</i> (<i>Physcomitrella) patens</i>

description: Plant glutamate receptor homologs (GLRs), which function as key calcium channels, play pivotal roles in various developmental processes as well as stress responses. The moss <i>Physcomitrium patens</i>, a representative of the earliest land plant lineage, possess multiple pathways of hormone signaling for coordinating growth and adaptation responses. However, it is not clear whether GLRs are connected to hormone-mediated growth control in the moss. In this study, we report that one of the two GLRs in <i>P. patens</i>, PpGLR1, involves in abscisic acid (ABA)-mediated growth regulation. ABA represses the growth of wild-type moss, and intriguingly, the <i>PpGLR1</i> transcript levels are significantly increased in response to ABA treatment, based on both gene expression and the <i>PpGLR1pro::GUS</i> reporter results. Furthermore, the growth of <i>Ppglr1</i> knockout moss mutants is hypersensitive to ABA treatment. These results suggest that PpGLR1 plays a critical role in ABA-mediated growth regulation, which provide useful information for our further investigation of the regulatory mechanism between Ca<sup>2+</sup> signal and ABA in moss growth control.
DOI: 10.6084/m9.figshare.20254556
title: Ultrastructure change and transcriptome analysis of GA3 treatment on seed germination of moso bamboo(<i>Phyllostachys edulis</i>)

description: Exploring the mechanism of Gibberellic acid (GA<sub>3</sub>) treatment on seed germination of moso bamboo can lay a foundation for its future breeding and research. In this study, the germination-related indicators (germination rate, germination potential, vigor index, respiration rate) with different content of GA<sub>3</sub> treatment were measured, and the ultrastructure of moso bamboo seeds treated with low and high GA<sub>3</sub> concentrations was observed during the germination process. In addition, the transcriptome data of the germination seeds, with and without GA<sub>3</sub> treatment were analyzed. The results showed that the low GA<sub>3</sub> concentration (10 mol/L) increased the germination rate, germination potential, vigor index and respiration rate, thus promoting the germination of moso bamboo seeds, but a high concentration of GA<sub>3</sub> (50 mol/L) inhibited the seed germination. The low GA<sub>3</sub> concentration accelerated the decomposition of starch and fat and promoted the vacuole formation of cells, but the high GA<sub>3</sub> concentration damaged organelles and increased the endocytosis of cells. Compared with untreated moso bamboo seeds, the seeds had fewer genes expressed after GA<sub>3</sub> treatment. Starch and carbon metabolism play a very important role in seed development and embryo viability, whether the seed is treated with GA<sub>3</sub> or not. After hormone treatment, GID1 and DELLA-related genes homologous to rice genes is not expressed, but the expression of PIF4, PIF5, GA<sub>3</sub> <i>ox</i>2, GA<sub>2</sub><i>oxs</i>, etc., were up-regulated.
DOI: 10.6084/m9.figshare.20254556.v1
title: Ultrastructure change and transcriptome analysis of GA3 treatment on seed germination of moso bamboo(<i>Phyllostachys edulis</i>)

description: Exploring the mechanism of Gibberellic acid (GA<sub>3</sub>) treatment on seed germination of moso bamboo can lay a foundation for its future breeding and research. In this study, the germination-related indicators (germination rate, germination potential, vigor index, respiration rate) with different content of GA<sub>3</sub> treatment were measured, and the ultrastructure of moso bamboo seeds treated with low and high GA<sub>3</sub> concentrations was observed during the germination process. In addition, the transcriptome data of the germination seeds, with and without GA<sub>3</sub> treatment were analyzed. The results showed that the low GA<sub>3</sub> concentration (10 mol/L) increased the germination rate, germination potential, vigor index and respiration rate, thus promoting the germination of moso bamboo seeds, but a high concentration of GA<sub>3</sub> (50 mol/L) inhibited the seed germination. The low GA<sub>3</sub> concentration accelerated the decomposition of starch and fat and promoted the vacuole formation of cells, but the high GA<sub>3</sub> concentration damaged organelles and increased the endocytosis of cells. Compared with untreated moso bamboo seeds, the seeds had fewer genes expressed after GA<sub>3</sub> treatment. Starch and carbon metabolism play a very important role in seed development and embryo viability, whether the seed is treated with GA<sub>3</sub> or not. After hormone treatment, GID1 and DELLA-related genes homologous to rice genes is not expressed, but the expression of PIF4, PIF5, GA<sub>3</sub> <i>ox</i>2, GA<sub>2</sub><i>oxs</i>, etc., were up-regulated.
DOI: 10.6084/m9.figshare.18933642.v1
title: Genome-wide identification and expression pattern analysis of the TCP transcription factor family in <i>Ginkgo biloba</i>

description: Plant-specific TCP transcription factors play an essential role in plant growth and development. They can regulate leaf curvature, flower symmetry and the synthesis of secondary metabolites. The flavonoids in <i>Ginkgo biloba</i> leaf are one of the main medicinally bioactivate compounds, which have pharmacological and beneficial health effects for humans. In this study, a total of 13 <i>TCP</i> genes were identified in <i>G. biloba</i>, and 5 of them belonged to PCF subclades (<i>GbTCP03, GbTCP07, GbTCP05, GbTCP13, GbTCP02</i>) while others belonged to CIN (<i>GbTCP01, GbTCP04, GbTCP06, GbTCP08, GbTCP09, GbTCP10, GbTCP11, GbTCP12</i>) subclades according to phylogenetic analysis. Numerous <i>cis</i>-acting elements related to various biotic and abiotic signals were predicted on the promoters by <i>cis</i>-element analysis, suggesting that the expression of <i>GbTCPs</i> might be co-regulated by multiple signals. Transcript abundance analysis exhibited that most of <i>GbTCPs</i> responded to multiple phytohormones. Among them, the relative expression levels of <i>GbTCP06, GbTCP11</i>, and <i>GbTCP13</i> were found to be significantly influenced by exogenous ABA, SA and MeJA application. In addition, a total of 126 miRNAs were predicted to target 9 <i>TCPs</i> (including <i>GbTCP01, GbTCP02, GbTCP04, GbTCP05, GbTCP06, GbTCP08, GbTCP11, GbTCP12, GbTCP13</i>). The correlation analysis between the expression level of <i>GbTCPs</i> and the flavonoid contents showed that <i>GbTCP03, GbTCP04, GbTCP07</i> might involve in flavonoid biosynthesis in <i>G. biloba</i>. In short, this study mainly provided a theoretical foundation for better understanding the potential function of <i>TCPs</i> in <i>G. biloba</i>.
DOI: 10.6084/m9.figshare.18933642
title: Genome-wide identification and expression pattern analysis of the TCP transcription factor family in <i>Ginkgo biloba</i>

description: Plant-specific TCP transcription factors play an essential role in plant growth and development. They can regulate leaf curvature, flower symmetry and the synthesis of secondary metabolites. The flavonoids in <i>Ginkgo biloba</i> leaf are one of the main medicinally bioactivate compounds, which have pharmacological and beneficial health effects for humans. In this study, a total of 13 <i>TCP</i> genes were identified in <i>G. biloba</i>, and 5 of them belonged to PCF subclades (<i>GbTCP03, GbTCP07, GbTCP05, GbTCP13, GbTCP02</i>) while others belonged to CIN (<i>GbTCP01, GbTCP04, GbTCP06, GbTCP08, GbTCP09, GbTCP10, GbTCP11, GbTCP12</i>) subclades according to phylogenetic analysis. Numerous <i>cis</i>-acting elements related to various biotic and abiotic signals were predicted on the promoters by <i>cis</i>-element analysis, suggesting that the expression of <i>GbTCPs</i> might be co-regulated by multiple signals. Transcript abundance analysis exhibited that most of <i>GbTCPs</i> responded to multiple phytohormones. Among them, the relative expression levels of <i>GbTCP06, GbTCP11</i>, and <i>GbTCP13</i> were found to be significantly influenced by exogenous ABA, SA and MeJA application. In addition, a total of 126 miRNAs were predicted to target 9 <i>TCPs</i> (including <i>GbTCP01, GbTCP02, GbTCP04, GbTCP05, GbTCP06, GbTCP08, GbTCP11, GbTCP12, GbTCP13</i>). The correlation analysis between the expression level of <i>GbTCPs</i> and the flavonoid contents showed that <i>GbTCP03, GbTCP04, GbTCP07</i> might involve in flavonoid biosynthesis in <i>G. biloba</i>. In short, this study mainly provided a theoretical foundation for better understanding the potential function of <i>TCPs</i> in <i>G. biloba</i>.
DOI: 10.6084/m9.figshare.21393993
title: The characterization and expression analysis under stress conditions of <i>PCST1</i> in <i>Arabidopsis</i>

description: Analysis of <i>PCST1</i> expression characteristics and the role of <i>PCST1</i> in response to osmotic stress in <i>Arabidopsis thaliana</i>. The structure of <i>PCST1</i> was analyzed using Bioinformatics method. Real-time PCR, GUS tissue localization and subcellular localization were adopted to analyze the expression pattern of <i>PCST1</i> in Arabidopsis. To validate the transgenic positive strain of <i>PCST1</i> using Real-time PCR, overexpression experiments were performed in wild type. Full-length cDNA was cloned and connected into a binary vector with 35S promoter, and the construction was transformed into wild type. With NaCl and mannitol treatments, the germination rate, green leaves rate, physiological indexes were carried out and counted in Arabidopsis with overexpression of <i>PCST1</i> and T-DNA insertion mutants. The molecular mechanism of <i>PCST1</i> in response to osmotic stress in Arabidopsis was analyzed. Based on the bioinformatic analysis, PCST1 is a hydrophobin with 403 amino acids, and the molecular weight is 45.3236 KDa. It contains only the START (the lipid/sterol – binding StAR – related lipid transfer protein domains) conservative domain. PCST1 possesses phosphatidylcholine binding sites and transmembrane region. Expression pattern analysis showed that expression of <i>PCST1</i> increased with time. The <i>PCST1</i> widely expressed in Arabidopsis, including roots, axils of stem leaves, flowers (sepal, conductive tissue of the petal, thrum, anther and stigmas), and the top and basal parts of the siliquas. It mainly localized in cell membrane. The overexpression of <i>PCST1</i> enhanced the sensitivity to osmotic stress in <i>Arabidopsis</i> based on the germination rate. While expression of <i>PCST1</i> decreased, and the sensitivity to osmotic stress had no obvious change in Arabidopsis. Its molecular mechanism study showed, that PCST1 response to osmotic stress resistance by regulating the proline, betaine synthesis, as well as the expression of key genes <i>SOS, NCED, CIPK</i>. PCST1 is composed of 403 amino acids. The START conservative domain, a transmembrane structure, the phosphatidyl choline binding sites are contained in PCST1. It is localized in cytoplasmic membrane. The <i>PCST1</i> widely expressed in the root, leaf, flower and siliquas. NaCl and mannitol suppressed the expression of <i>PCST1</i> and PCST1 can negatively control action of <i>Arabidopsis</i> in the osmotic stress. PCST1 regulates the synthetic pathway of proline, betaine and the expression of <i>SOS, NCED</i> and <i>CIPK</i> in response to the osmotic stress resistance.
DOI: 10.6084/m9.figshare.21393993.v1
title: The characterization and expression analysis under stress conditions of <i>PCST1</i> in <i>Arabidopsis</i>

description: Analysis of <i>PCST1</i> expression characteristics and the role of <i>PCST1</i> in response to osmotic stress in <i>Arabidopsis thaliana</i>. The structure of <i>PCST1</i> was analyzed using Bioinformatics method. Real-time PCR, GUS tissue localization and subcellular localization were adopted to analyze the expression pattern of <i>PCST1</i> in Arabidopsis. To validate the transgenic positive strain of <i>PCST1</i> using Real-time PCR, overexpression experiments were performed in wild type. Full-length cDNA was cloned and connected into a binary vector with 35S promoter, and the construction was transformed into wild type. With NaCl and mannitol treatments, the germination rate, green leaves rate, physiological indexes were carried out and counted in Arabidopsis with overexpression of <i>PCST1</i> and T-DNA insertion mutants. The molecular mechanism of <i>PCST1</i> in response to osmotic stress in Arabidopsis was analyzed. Based on the bioinformatic analysis, PCST1 is a hydrophobin with 403 amino acids, and the molecular weight is 45.3236 KDa. It contains only the START (the lipid/sterol – binding StAR – related lipid transfer protein domains) conservative domain. PCST1 possesses phosphatidylcholine binding sites and transmembrane region. Expression pattern analysis showed that expression of <i>PCST1</i> increased with time. The <i>PCST1</i> widely expressed in Arabidopsis, including roots, axils of stem leaves, flowers (sepal, conductive tissue of the petal, thrum, anther and stigmas), and the top and basal parts of the siliquas. It mainly localized in cell membrane. The overexpression of <i>PCST1</i> enhanced the sensitivity to osmotic stress in <i>Arabidopsis</i> based on the germination rate. While expression of <i>PCST1</i> decreased, and the sensitivity to osmotic stress had no obvious change in Arabidopsis. Its molecular mechanism study showed, that PCST1 response to osmotic stress resistance by regulating the proline, betaine synthesis, as well as the expression of key genes <i>SOS, NCED, CIPK</i>. PCST1 is composed of 403 amino acids. The START conservative domain, a transmembrane structure, the phosphatidyl choline binding sites are contained in PCST1. It is localized in cytoplasmic membrane. The <i>PCST1</i> widely expressed in the root, leaf, flower and siliquas. NaCl and mannitol suppressed the expression of <i>PCST1</i> and PCST1 can negatively control action of <i>Arabidopsis</i> in the osmotic stress. PCST1 regulates the synthetic pathway of proline, betaine and the expression of <i>SOS, NCED</i> and <i>CIPK</i> in response to the osmotic stress resistance.
DOI: 10.6084/m9.figshare.18319446
title: Gravity induces asymmetric Ca<sup>2+</sup> spikes in the root cap in the early stage of gravitropism

description: Gravitropism is an important strategy for the adaptation of plants to the changing environment. Previous reports indicated that Ca<sup>2+</sup> participated in plant gravity response. However, present information on the functions of Ca<sup>2+</sup> in plant gravitropism was obtained mainly on coleoptiles, hypocotyls, and petioles, little is known about the dynamic changes of Ca<sup>2+</sup> during root gravitropism. In the present study, the transgenic <i>Arabidopsis thaliana</i> R-GECO1 was placed horizontally and subsequently vertically on a refitted Leica SP8 laser scanning confocal microscopy with a vertical stage. Real-time observations indicated that gravistimulation induced not only an increase in the Ca<sup>2+</sup> concentration, but also an accelerated occurrence of Ca<sup>2+</sup> sparks in the root cap, especially in the lower side of the lateral root cap, indicating a strong tie between Ca<sup>2+</sup> dynamics and gravistimulation during the early stage of root gravity response.
DOI: 10.6084/m9.figshare.18319446.v1
title: Gravity induces asymmetric Ca<sup>2+</sup> spikes in the root cap in the early stage of gravitropism

description: Gravitropism is an important strategy for the adaptation of plants to the changing environment. Previous reports indicated that Ca<sup>2+</sup> participated in plant gravity response. However, present information on the functions of Ca<sup>2+</sup> in plant gravitropism was obtained mainly on coleoptiles, hypocotyls, and petioles, little is known about the dynamic changes of Ca<sup>2+</sup> during root gravitropism. In the present study, the transgenic <i>Arabidopsis thaliana</i> R-GECO1 was placed horizontally and subsequently vertically on a refitted Leica SP8 laser scanning confocal microscopy with a vertical stage. Real-time observations indicated that gravistimulation induced not only an increase in the Ca<sup>2+</sup> concentration, but also an accelerated occurrence of Ca<sup>2+</sup> sparks in the root cap, especially in the lower side of the lateral root cap, indicating a strong tie between Ca<sup>2+</sup> dynamics and gravistimulation during the early stage of root gravity response.
DOI: 10.6084/m9.figshare.19174583
title: Plant elicitor peptide 1 fortifies root cell walls and triggers a systemic root-to-shoot immune signaling in <i>Arabidopsis</i>

description: Plant immunity is initiated by cell surface-localized receptors upon perception of pathogen-derived microbe or pathogen-associated molecular patterns (MAMPs/PAMPs), damage/danger-associated molecular patterns (DAMPs), and phytocytokines. Different patterns activate highly overlapping immune signaling at the early stage but divergent physiological responses at the late stage. Here, we indicate that plant elicitor peptide 1 (Pep1), a well-known DAMP, induces lignin and callose depositions, two types of late immune responses for strengthening the plant cell wall. Pep1-induced lignin and callose depositions in <i>Arabidopsis</i> root rely on early signaling components for Pep1 perception and signaling propagation. The phytohormone jasmonic acid and ethylene differently regulate the Pep1-regulated cell wall consolidation. Pep1 application in root also triggers a systemic immune signaling in shoot, and reactive oxygen species (ROS) is essential for the signaling communication between root and shoot. Collectively, the study reveals that Pep1 strengthens cell walls in root and triggers a systemic immune signaling from root to shoot.
DOI: 10.6084/m9.figshare.19174583.v1
title: Plant elicitor peptide 1 fortifies root cell walls and triggers a systemic root-to-shoot immune signaling in <i>Arabidopsis</i>

description: Plant immunity is initiated by cell surface-localized receptors upon perception of pathogen-derived microbe or pathogen-associated molecular patterns (MAMPs/PAMPs), damage/danger-associated molecular patterns (DAMPs), and phytocytokines. Different patterns activate highly overlapping immune signaling at the early stage but divergent physiological responses at the late stage. Here, we indicate that plant elicitor peptide 1 (Pep1), a well-known DAMP, induces lignin and callose depositions, two types of late immune responses for strengthening the plant cell wall. Pep1-induced lignin and callose depositions in <i>Arabidopsis</i> root rely on early signaling components for Pep1 perception and signaling propagation. The phytohormone jasmonic acid and ethylene differently regulate the Pep1-regulated cell wall consolidation. Pep1 application in root also triggers a systemic immune signaling in shoot, and reactive oxygen species (ROS) is essential for the signaling communication between root and shoot. Collectively, the study reveals that Pep1 strengthens cell walls in root and triggers a systemic immune signaling from root to shoot.