cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25752510.v1
title: Investigation of <i>Arabidopsis</i> root skototropism with different distance settings

description: Plants can activate protective and defense mechanisms under biotic and abiotic stresses. Their roots naturally grow in the soil, but when they encounter sunlight in the top-soil layers, they may move away from the light source to seek darkness. Here we investigate the skototropic behavior of roots, which promotes their fitness and survival. Glutamate-like receptors (GLRs) of plants play roles in sensing and responding to signals, but their role in root skototropism is not yet understood. Light-induced tropisms are known to be affected by auxin distribution, mainly determined by auxin efflux proteins (PIN proteins) at the root tip. However, the role of PIN proteins in root skototropism has not been investigated yet. To better understand root skototropism and its connection to the distance between roots and light, we established five distance settings between seedlings and darkness to investigate the variations in root bending tendencies. We compared differences in root skototropic behavior across different expression lines of <i>Arabidopsis thaliana</i> seedlings (<i>atglr3.7 ko, AtGLR3.7 OE</i>, and <i>pin2 knockout</i>) to comprehend their functions. Our research shows that as the distance between roots and darkness increases, the root’s positive skototropism noticeably weakens. Our findings highlight the involvement of GLR3.7 and PIN2 in root skototropism.
DOI: 10.6084/m9.figshare.c.3637250_d7.v1
title: Additional file 2: Table S2. of Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana

description: Microarray data of genes with lower expression levels (FC
DOI: 10.6084/m9.figshare.c.3637250_d6.v1
title: Additional file 1: Table S1. of Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana

description: Microarray data of genes with higher expression levels (FC &gt; 1.3, p
DOI: 10.6084/m9.figshare.25976890
title: Artificial and biological supports are different for pea plants

description: Previous studies on the kinematics of pea plants’ ascent and attach behavior have demonstrated that the signature of their movement varies depending on the kind of support. So far, these studies have been confined to artificial supports (e.g. wooden sticks). Little is known regarding the conditions under which pea plants could rely on biological supports (e.g. neighboring plants) for climbing toward the light. In this study, we capitalize on the 3D kinematic analysis of movement to ascertain whether pea plants scale their kinematics differently depending on whether they aim for artificial or biological support. Results suggest that biological support determines a smoother and more accurate behavior than that elicited by the artificial one. These results shed light on pea plants’ ability to detect and classify the properties of objects and implement a movement plan attuned to the very nature of the support. We contend that such differences depend on the augmented multisensory experience elicited by the biological support.
DOI: 10.6084/m9.figshare.25976890.v1
title: Artificial and biological supports are different for pea plants

description: Previous studies on the kinematics of pea plants’ ascent and attach behavior have demonstrated that the signature of their movement varies depending on the kind of support. So far, these studies have been confined to artificial supports (e.g. wooden sticks). Little is known regarding the conditions under which pea plants could rely on biological supports (e.g. neighboring plants) for climbing toward the light. In this study, we capitalize on the 3D kinematic analysis of movement to ascertain whether pea plants scale their kinematics differently depending on whether they aim for artificial or biological support. Results suggest that biological support determines a smoother and more accurate behavior than that elicited by the artificial one. These results shed light on pea plants’ ability to detect and classify the properties of objects and implement a movement plan attuned to the very nature of the support. We contend that such differences depend on the augmented multisensory experience elicited by the biological support.
DOI: 10.6084/m9.figshare.26413411
title: CLE peptides act via the receptor-like kinase CRINKLY 4 in <i>Physcomitrium patens</i> gametophore development

description: The CLAVATA pathway plays a key role in the regulation of multicellular shoot and root meristems in flowering plants. In Arabidopsis, CLAVATA 3-like signaling peptides (CLEs) act via receptor-like kinases CLAVATA 1 and CRINKLY 4 (CR4). In the moss <i>Physcomitrium patens</i>, PpCLAVATA and PpCR4 were previously studied independently and shown to play conserved roles in the regulation of cell proliferation and differentiation. The plant calpain DEFECTIVE KERNEL 1 (DEK1) has been identified as another key regulator of cell division and cell fate in vascular plants and bryophytes. The functional interaction between CLAVATA, CR4, and DEK1 remains unknown. Here, we show that <i>P. patens crinkly4</i> and <i>dek1</i> mutants respond differently to CLE peptide treatments suggesting their distinct roles in the CLAVATA pathway. Reduced CLAVATA-mediated suppression of leafy shoot growth in <i>Δcr4</i> mutants indicates that PpCR4 is involved in CLV3p perception, most likely as a receptor. The CLV3p strongly suppressed leaf vein development in <i>Δcr4</i> mutants, suggesting that other receptors are involved in these processes and indicating a potential role of PpCR4 in organ sensitization to CLEs.
DOI: 10.6084/m9.figshare.26413411.v1
title: CLE peptides act via the receptor-like kinase CRINKLY 4 in <i>Physcomitrium patens</i> gametophore development

description: The CLAVATA pathway plays a key role in the regulation of multicellular shoot and root meristems in flowering plants. In Arabidopsis, CLAVATA 3-like signaling peptides (CLEs) act via receptor-like kinases CLAVATA 1 and CRINKLY 4 (CR4). In the moss <i>Physcomitrium patens</i>, PpCLAVATA and PpCR4 were previously studied independently and shown to play conserved roles in the regulation of cell proliferation and differentiation. The plant calpain DEFECTIVE KERNEL 1 (DEK1) has been identified as another key regulator of cell division and cell fate in vascular plants and bryophytes. The functional interaction between CLAVATA, CR4, and DEK1 remains unknown. Here, we show that <i>P. patens crinkly4</i> and <i>dek1</i> mutants respond differently to CLE peptide treatments suggesting their distinct roles in the CLAVATA pathway. Reduced CLAVATA-mediated suppression of leafy shoot growth in <i>Δcr4</i> mutants indicates that PpCR4 is involved in CLV3p perception, most likely as a receptor. The CLV3p strongly suppressed leaf vein development in <i>Δcr4</i> mutants, suggesting that other receptors are involved in these processes and indicating a potential role of PpCR4 in organ sensitization to CLEs.
DOI: 10.6084/m9.figshare.25883767
title: Genome-wide identification of <i>YABBY</i> gene family and its expression pattern analysis in <i>Astragalus mongholicus</i>

description: During plant growth and development, the <i>YABBY</i> gene plays a crucial role in the morphological structure, hormone signaling, stress resistance, crop breeding, and agricultural production of plant lateral organs, leaves, flowers, and fruits. <i>Astragalus mongholicus</i> is a perennial herbaceous plant in the legume family, widely used worldwide due to its high medicinal and edible value. However, there have been no reports of the <i>YABBY</i> gene family in <i>A. mongholicus</i>. This study used bioinformatics methods, combined with databases and analysis websites, to systematically analyze the <i>AmYABBY</i> gene family in the entire genome of <i>A. mongholicus</i> and verified its expression patterns in different tissues of <i>A. mongholicus</i> through transcriptome data and qRT-PCR experiments. A total of seven <i>AmYABBY</i> genes were identified, which can be divided into five subfamilies and distributed on three chromosomes. Two pairs of <i>AmYABBY</i> genes may be involved in fragment duplication on three chromosomes. All AmYABBY proteins have a zinc finger YABBY domain, and members of the same group have similar motif composition and intron – exon structure. In the promoter region of the genes, light-responsive and MeJa-response <i>cis</i>-elements are dominant. <i>AmYABBY</i> is highly expressed in stems and leaves, especially <i>AmYABBY1</i>, <i>AmYABBY2</i>, and <i>AmYABBY3</i>, which play important roles in the growth and development of stems and leaves. The <i>AmYABBY</i> gene family regulates the growth and development of <i>A. mongholicus</i>. In summary, this study provides a theoretical basis for in-depth research on the function of the <i>AmYABBY</i> gene and new insights into the molecular response mechanism of the growth and development of the traditional Chinese medicine <i>A. mongholicus</i>.
DOI: 10.6084/m9.figshare.25883767.v1
title: Genome-wide identification of <i>YABBY</i> gene family and its expression pattern analysis in <i>Astragalus mongholicus</i>

description: During plant growth and development, the <i>YABBY</i> gene plays a crucial role in the morphological structure, hormone signaling, stress resistance, crop breeding, and agricultural production of plant lateral organs, leaves, flowers, and fruits. <i>Astragalus mongholicus</i> is a perennial herbaceous plant in the legume family, widely used worldwide due to its high medicinal and edible value. However, there have been no reports of the <i>YABBY</i> gene family in <i>A. mongholicus</i>. This study used bioinformatics methods, combined with databases and analysis websites, to systematically analyze the <i>AmYABBY</i> gene family in the entire genome of <i>A. mongholicus</i> and verified its expression patterns in different tissues of <i>A. mongholicus</i> through transcriptome data and qRT-PCR experiments. A total of seven <i>AmYABBY</i> genes were identified, which can be divided into five subfamilies and distributed on three chromosomes. Two pairs of <i>AmYABBY</i> genes may be involved in fragment duplication on three chromosomes. All AmYABBY proteins have a zinc finger YABBY domain, and members of the same group have similar motif composition and intron – exon structure. In the promoter region of the genes, light-responsive and MeJa-response <i>cis</i>-elements are dominant. <i>AmYABBY</i> is highly expressed in stems and leaves, especially <i>AmYABBY1</i>, <i>AmYABBY2</i>, and <i>AmYABBY3</i>, which play important roles in the growth and development of stems and leaves. The <i>AmYABBY</i> gene family regulates the growth and development of <i>A. mongholicus</i>. In summary, this study provides a theoretical basis for in-depth research on the function of the <i>AmYABBY</i> gene and new insights into the molecular response mechanism of the growth and development of the traditional Chinese medicine <i>A. mongholicus</i>.
DOI: 10.6084/m9.figshare.c.3637250_d1.v1
title: Additional file 3: Table S3. of Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana

description: Microarray data of genes with lower expression levels (&lt;0.74, p
DOI: 10.6084/m9.figshare.24926655
title: Reciprocal modulation of responses to nitrate starvation and hypoxia in roots and leaves of <i>Arabidopsis thaliana</i>

description: The flooding of agricultural land leads to hypoxia and nitrate leaching. While understanding the plant’s response to these conditions is essential for crop improvement, the effect of extended nitrate limitation on subsequent hypoxia has not been studied in an organ-specific manner. We cultivated <i>Arabidopsis thaliana</i> without nitrate for 1 week before inducing hypoxia by bubbling the hydroponic solution with nitrogen gas for 16 h. In the roots, the transcripts of two transcription factor genes (<i>HRA1</i>, <i>HRE2</i>) and three genes involved in fermentation (<i>SUS4</i>, <i>PDC1</i>, <i>ADH1</i>) were ~10- to 100-fold upregulated by simultaneous hypoxia and nitrate starvation compared to the control condition (replete nitrate and oxygen). In contrast, this hypoxic upregulation was ~5 to 10 times stronger when nitrate was available. The phytoglobin genes <i>PGB1</i> and <i>PGB2</i>, involved in nitric oxide (NO) scavenging, were massively downregulated by nitrate starvation (~1000-fold and 10<sup>5</sup>-fold, respectively), but only under ambient oxygen levels; this was reflected in a 2.5-fold increase in NO concentration. In the leaves, <i>HRA1</i>, <i>SUS4</i>, and <i>RAP2.3</i> were upregulated ~20-fold by hypoxia under nitrate starvation, whereas this upregulation was virtually absent in the presence of nitrate. Our results highlight that the plant’s responses to nitrate starvation and hypoxia can influence each other.
DOI: 10.6084/m9.figshare.24926655.v1
title: Reciprocal modulation of responses to nitrate starvation and hypoxia in roots and leaves of <i>Arabidopsis thaliana</i>

description: The flooding of agricultural land leads to hypoxia and nitrate leaching. While understanding the plant’s response to these conditions is essential for crop improvement, the effect of extended nitrate limitation on subsequent hypoxia has not been studied in an organ-specific manner. We cultivated <i>Arabidopsis thaliana</i> without nitrate for 1 week before inducing hypoxia by bubbling the hydroponic solution with nitrogen gas for 16 h. In the roots, the transcripts of two transcription factor genes (<i>HRA1</i>, <i>HRE2</i>) and three genes involved in fermentation (<i>SUS4</i>, <i>PDC1</i>, <i>ADH1</i>) were ~10- to 100-fold upregulated by simultaneous hypoxia and nitrate starvation compared to the control condition (replete nitrate and oxygen). In contrast, this hypoxic upregulation was ~5 to 10 times stronger when nitrate was available. The phytoglobin genes <i>PGB1</i> and <i>PGB2</i>, involved in nitric oxide (NO) scavenging, were massively downregulated by nitrate starvation (~1000-fold and 10<sup>5</sup>-fold, respectively), but only under ambient oxygen levels; this was reflected in a 2.5-fold increase in NO concentration. In the leaves, <i>HRA1</i>, <i>SUS4</i>, and <i>RAP2.3</i> were upregulated ~20-fold by hypoxia under nitrate starvation, whereas this upregulation was virtually absent in the presence of nitrate. Our results highlight that the plant’s responses to nitrate starvation and hypoxia can influence each other.
DOI: 10.6084/m9.figshare.25145050
title: Endogenous cAMP elevation in <i>Brassica napus</i> causes changes in phytohormone levels

description: In higher plants, the regulatory roles of cAMP (cyclic adenosine 3′,5′-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (<i>Brassica napus</i> L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of <i>TAA1</i> and <i>CYP83B1</i> in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of <i>PR4</i> and <i>KIN2</i> expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
DOI: 10.6084/m9.figshare.25145050.v1
title: Endogenous cAMP elevation in <i>Brassica napus</i> causes changes in phytohormone levels

description: In higher plants, the regulatory roles of cAMP (cyclic adenosine 3′,5′-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (<i>Brassica napus</i> L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of <i>TAA1</i> and <i>CYP83B1</i> in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of <i>PR4</i> and <i>KIN2</i> expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.
DOI: 10.6084/m9.figshare.25955915
title: Identification and expression profiling of microRNAs in leaf tissues of <i>Foeniculum vulgare</i> Mill. under salinity stress

description: <i>Foeniculum vulgare</i> Mill. commonly known as fennel, is a globally recognized aromatic medicinal plant and culinary herb with widespread popularity due to its antimicrobial, antioxidant, carminative, and diuretic properties, among others. Although the phenotypic effects of salinity stress have been previously explored in fennel, the molecular mechanisms underlying responses to elevated salinity in this plant remain elusive. MicroRNAs (miRNAs) are tiny, endogenous, and extensively conserved non-coding RNAs (ncRNAs) typically ranging from 20 to 24 nucleotides (nt) in length that play a major role in a myriad of biological functions. In fact, a number of miRNAs have been extensively associated with responses to abiotic stress in plants. Consequently, employing computational methodologies and rigorous filtering criteria, 40 putative miRNAs belonging to 25 different families were characterized from fennel in this study. Subsequently, employing the psRNATarget tool, a total of 67 different candidate target transcripts for the characterized fennel miRNAs were predicted. Additionally, the expression patterns of six selected fennel miRNAs (i.e. fvu-miR156a, fvu-miR162a-3p, fvu-miR166a-3p, fvu-miR167a-5p, fvu-miR171a-3p, and fvu-miR408-3p) were analyzed under salinity stress conditions via qPCR. This article holds notable significance as it identifies not only 40 putative miRNAs in fennel, a non-model plant, but also pioneers the analysis of their expression under salinity stress conditions.
DOI: 10.6084/m9.figshare.25955915.v1
title: Identification and expression profiling of microRNAs in leaf tissues of <i>Foeniculum vulgare</i> Mill. under salinity stress

description: <i>Foeniculum vulgare</i> Mill. commonly known as fennel, is a globally recognized aromatic medicinal plant and culinary herb with widespread popularity due to its antimicrobial, antioxidant, carminative, and diuretic properties, among others. Although the phenotypic effects of salinity stress have been previously explored in fennel, the molecular mechanisms underlying responses to elevated salinity in this plant remain elusive. MicroRNAs (miRNAs) are tiny, endogenous, and extensively conserved non-coding RNAs (ncRNAs) typically ranging from 20 to 24 nucleotides (nt) in length that play a major role in a myriad of biological functions. In fact, a number of miRNAs have been extensively associated with responses to abiotic stress in plants. Consequently, employing computational methodologies and rigorous filtering criteria, 40 putative miRNAs belonging to 25 different families were characterized from fennel in this study. Subsequently, employing the psRNATarget tool, a total of 67 different candidate target transcripts for the characterized fennel miRNAs were predicted. Additionally, the expression patterns of six selected fennel miRNAs (i.e. fvu-miR156a, fvu-miR162a-3p, fvu-miR166a-3p, fvu-miR167a-5p, fvu-miR171a-3p, and fvu-miR408-3p) were analyzed under salinity stress conditions via qPCR. This article holds notable significance as it identifies not only 40 putative miRNAs in fennel, a non-model plant, but also pioneers the analysis of their expression under salinity stress conditions.