cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24043243.v1
title: Dynamic changes in the levels of metabolites and endogenous hormones during the germination of <i>Zanthoxylum nitidum</i> (Roxb.) DC. Seeds

description: Accumulating experimental data have shown that endogenous hormones play important roles in regulating seed dormancy and germination. <i>Zanthoxylum nitidum</i> is a medicinal plant that propagates via seeds, which require a long dormancy period for normal germination, and complex changes in metabolites occur during the germination process. However, the regulatory network of endogenous hormones and metabolites during the germination of <i>Z. nitidum</i> seeds remains unclear. This study investigated the dynamic changes in the levels of metabolites and endogenous hormones during the germination of <i>Z. nitidum</i> seeds. The results revealed an increase in the levels of gibberellin 3 (GA<sub>3</sub>), 12-oxophytodienoic acid (OPDA), 1-aminocyclopropane-1-carboxylic acid (ACC) and trans-zeatin (TZ) and decrease in the levels of abscisic acid (ABA), jasmonic acid (JA), <i>N</i>-[(-)-jasmonoyl]-(S)-isoleucine (JA-Ile) and trans-zeatin riboside (TZR). Overall, 112 differential metabolites (DAMs) were screened from 3 seed samples (Sa, Sb and Sc), most of which are related to primary metabolism. A total of 16 DAMs (including 3 monosaccharides, 3 phosphate lipids, 3 carboxylic acids, 1 amino acid, 2 pyrimidines, and 4 nucleotides) were identified in the three sample comparison pairs (Sa vs Sb, Sa vs Sc, and Sb vs Sc); these DAMs were significantly enriched in purine metabolism; glycerophospholipid metabolism, citrate cycle (TCA cycle), alanine, aspartate and glutamate metabolism and pyruvate metabolism. OPDA, ACC and GAs were significantly positively correlated with upregulated metabolites, whereas ABA and JA were significantly positively correlated with downregulated metabolites. Finally, a hypothetical metabolic network of endogenous hormones that regulate seed germination was constructed. This study deepens our understanding of the importance of endogenous hormonal profiles that mediate seed germination.
DOI: 10.6084/m9.figshare.21873603
title: Overexpression of the <i>Ginkgo biloba</i> dihydroflavonol 4-reductase gene <i>GbDFR6</i> results in the self-incompatibility-like phenotypes in transgenic tobacco

description: Although flavonoids play multiple roles in plant growth and development, the involvement in plant self-incompatibility (SI) have not been reported. In this research, the fertility of transgenic tobacco plants overexpressing the <i>Ginkgo biloba</i> dihydroflavonol 4-reductase gene, <i>GbDFR6</i>, were investigated. To explore the possible physiological defects leading to the failure of embryo development in transgenic tobacco plants, functions of pistils and pollen grains were examined. Transgenic pistils pollinated with pollen grains from another tobacco plants (either transgenic or wild-type), developed full of well-developed seeds. In contrast, in self-pollinated transgenic tobacco plants, pollen-tube growth was arrested in the upper part of the style, and small abnormal seeds developed without fertilization. Although the mechanism remains unclear, our research may provide a valuable method to create SI tobacco plants for breeding.
DOI: 10.6084/m9.figshare.21873603.v1
title: Overexpression of the <i>Ginkgo biloba</i> dihydroflavonol 4-reductase gene <i>GbDFR6</i> results in the self-incompatibility-like phenotypes in transgenic tobacco

description: Although flavonoids play multiple roles in plant growth and development, the involvement in plant self-incompatibility (SI) have not been reported. In this research, the fertility of transgenic tobacco plants overexpressing the <i>Ginkgo biloba</i> dihydroflavonol 4-reductase gene, <i>GbDFR6</i>, were investigated. To explore the possible physiological defects leading to the failure of embryo development in transgenic tobacco plants, functions of pistils and pollen grains were examined. Transgenic pistils pollinated with pollen grains from another tobacco plants (either transgenic or wild-type), developed full of well-developed seeds. In contrast, in self-pollinated transgenic tobacco plants, pollen-tube growth was arrested in the upper part of the style, and small abnormal seeds developed without fertilization. Although the mechanism remains unclear, our research may provide a valuable method to create SI tobacco plants for breeding.
DOI: 10.6084/m9.figshare.23385205
title: <i>ChIFNα</i> regulates adventitious root development in <i>Lotus japonicus</i> via an auxin-mediated pathway

description: Adventitious roots (ARs), developing from non-root tissue, play an important role in some plants. Here, the molecular mechanism of AR differentiation in <i>Lotus japonicus</i> L. (<i>L. japonicus</i>) with the transformed chicken interferon alpha gene (ChIFNα) encoding cytokine was studied. ChIFNα transgenic plants (TP) were identified by GUS staining, PCR, RT-PCR, and ELISA. Up to 0.175 μg/kg rChIFNα was detected in TP2 lines. Expressing rChIFNα promotes AR development by producing longer roots than controls. We found that the effect was enhanced with the auxin precursor IBA treatment in TP. IAA contents, POD, and PPO activities associated with auxin regulation were higher than wild type (WT) in TP and exogenous ChIFNα treatment plants. Transcriptome analysis revealed 48 auxin-related differentially expressed genes (DEGs) (FDR &lt; 0.05), which expression levels were verified by RT-qPCR analysis. GO enrichment analysis of DEGs also highlighted the auxin pathway. Further analysis found that ChIFNα significantly enhanced auxin synthesis and signaling mainly with up-regulated genes of ALDH, and GH3. Our study reveals that ChIFNα can promote plant AR development by mediating auxin regulation. The findings help explore the role of ChIFNα cytokines and expand animal gene sources for the molecular breeding of growth regulation of forage plants.
DOI: 10.6084/m9.figshare.23385205.v1
title: <i>ChIFNα</i> regulates adventitious root development in <i>Lotus japonicus</i> via an auxin-mediated pathway

description: Adventitious roots (ARs), developing from non-root tissue, play an important role in some plants. Here, the molecular mechanism of AR differentiation in <i>Lotus japonicus</i> L. (<i>L. japonicus</i>) with the transformed chicken interferon alpha gene (ChIFNα) encoding cytokine was studied. ChIFNα transgenic plants (TP) were identified by GUS staining, PCR, RT-PCR, and ELISA. Up to 0.175 μg/kg rChIFNα was detected in TP2 lines. Expressing rChIFNα promotes AR development by producing longer roots than controls. We found that the effect was enhanced with the auxin precursor IBA treatment in TP. IAA contents, POD, and PPO activities associated with auxin regulation were higher than wild type (WT) in TP and exogenous ChIFNα treatment plants. Transcriptome analysis revealed 48 auxin-related differentially expressed genes (DEGs) (FDR &lt; 0.05), which expression levels were verified by RT-qPCR analysis. GO enrichment analysis of DEGs also highlighted the auxin pathway. Further analysis found that ChIFNα significantly enhanced auxin synthesis and signaling mainly with up-regulated genes of ALDH, and GH3. Our study reveals that ChIFNα can promote plant AR development by mediating auxin regulation. The findings help explore the role of ChIFNα cytokines and expand animal gene sources for the molecular breeding of growth regulation of forage plants.
DOI: 10.6084/m9.figshare.23938035
title: Seedling growth and photosynthetic response of <i>Pterocarpus indicus</i> L. to shading stress

description: In tropical forests, the shade provided by tree canopies and extreme climate causes inhibition of plant seedling growth due to the lack of light. However, the plants can acclimate to such environmental stress by generating specific responses. The present study aimed to investigate the effects of shading conditions on ecophysiological performance of Narra seedlings (<i>Pterocarpus indicus</i> L.) via a mesocosm experiment. A pot experiment was conducted for 20 weeks in a greenhouse with different shading treatments, 75% (control), 25%, and 4% of full sunlight (FS). As a result, the photosynthetic rate (<i>P</i><sub>N</sub>), Rubisco enzyme activity, maximum carboxylation rate (<i>V</i><sub>Cmax</sub>), and maximum electron transport rate (<i>J</i><sub>max</sub>) in 25% FS treatment were higher or similar to those in control after three weeks of the beginning of shade treatment, whereas the highest values after ten weeks were observed in control. In contrast, the photosynthetic pigments were highest in control after three weeks, while the values were highest in 25% FS treatment after ten weeks. The growth parameters, such as biomass and leaf area, were highest in 75% FS treatment. The expression of Rubisco, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, and fructose-1,6-bisphosphatase were up-regulated in 4% FS treatment compared to control after ten weeks, contributing to tolerating the shade stress. Our findings indicated the capacity of <i>P. indicus</i> seedlings to tolerate and acclimate low light conditions causing shade stress by generating specific physiological and morphological responses, especially Rubisco enzyme activity as well as gene expression related to photosynthetic activity. The present study will improve our understanding of the tolerance mechanism of Narra plant under light-deficient conditions, thereby providing a better strategy for efficiently growing seedlings of this species in tropical rainforests.
DOI: 10.6084/m9.figshare.23938035.v1
title: Seedling growth and photosynthetic response of <i>Pterocarpus indicus</i> L. to shading stress

description: In tropical forests, the shade provided by tree canopies and extreme climate causes inhibition of plant seedling growth due to the lack of light. However, the plants can acclimate to such environmental stress by generating specific responses. The present study aimed to investigate the effects of shading conditions on ecophysiological performance of Narra seedlings (<i>Pterocarpus indicus</i> L.) via a mesocosm experiment. A pot experiment was conducted for 20 weeks in a greenhouse with different shading treatments, 75% (control), 25%, and 4% of full sunlight (FS). As a result, the photosynthetic rate (<i>P</i><sub>N</sub>), Rubisco enzyme activity, maximum carboxylation rate (<i>V</i><sub>Cmax</sub>), and maximum electron transport rate (<i>J</i><sub>max</sub>) in 25% FS treatment were higher or similar to those in control after three weeks of the beginning of shade treatment, whereas the highest values after ten weeks were observed in control. In contrast, the photosynthetic pigments were highest in control after three weeks, while the values were highest in 25% FS treatment after ten weeks. The growth parameters, such as biomass and leaf area, were highest in 75% FS treatment. The expression of Rubisco, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, and fructose-1,6-bisphosphatase were up-regulated in 4% FS treatment compared to control after ten weeks, contributing to tolerating the shade stress. Our findings indicated the capacity of <i>P. indicus</i> seedlings to tolerate and acclimate low light conditions causing shade stress by generating specific physiological and morphological responses, especially Rubisco enzyme activity as well as gene expression related to photosynthetic activity. The present study will improve our understanding of the tolerance mechanism of Narra plant under light-deficient conditions, thereby providing a better strategy for efficiently growing seedlings of this species in tropical rainforests.
DOI: 10.6084/m9.figshare.22338060
title: Drought resistance evaluation of sugar beet germplasms by response of phenotypic indicators

description: Sugar beet is a main sugar crop worldwide that often faces drought stress. The identification of drought tolerance of sugar beet germplasms is beneficial for breeding, but the research about it has been rarely reported. In this study, the drought tolerance of germplasms 92005-1, 94002-2 and 92021-1-1 was tested under simulated conditions. Seven days and 9% PEG treatment were the optimal conditions for evaluation, under which more phenotypic indicators showed significant difference in drought tolerance coefficient. The objective weighting and membership function method were established for evaluating the drought tolerance of different sugar beet germplasms. Drought stress decreased the biomass of leaves and roots of sugar beet germplasms. The drought-sensitive germplasm responded faster for leaf weight, root weight, plant height and root length. These indicators declined more significantly under long-term and severe stress. Increasing the root–shoot ratio and proline content were universal strategies of sugar beet germplasms to overcome drought stress. The drought-tolerant germplasms held higher peroxidase activity and better ability to scavenge reactive oxygen for preventing the damage.
DOI: 10.6084/m9.figshare.22338060.v1
title: Drought resistance evaluation of sugar beet germplasms by response of phenotypic indicators

description: Sugar beet is a main sugar crop worldwide that often faces drought stress. The identification of drought tolerance of sugar beet germplasms is beneficial for breeding, but the research about it has been rarely reported. In this study, the drought tolerance of germplasms 92005-1, 94002-2 and 92021-1-1 was tested under simulated conditions. Seven days and 9% PEG treatment were the optimal conditions for evaluation, under which more phenotypic indicators showed significant difference in drought tolerance coefficient. The objective weighting and membership function method were established for evaluating the drought tolerance of different sugar beet germplasms. Drought stress decreased the biomass of leaves and roots of sugar beet germplasms. The drought-sensitive germplasm responded faster for leaf weight, root weight, plant height and root length. These indicators declined more significantly under long-term and severe stress. Increasing the root–shoot ratio and proline content were universal strategies of sugar beet germplasms to overcome drought stress. The drought-tolerant germplasms held higher peroxidase activity and better ability to scavenge reactive oxygen for preventing the damage.
DOI: 10.6084/m9.figshare.23971690
title: Identification and expression analysis of MAPK cascade gene family in foxtail millet (<i>Setaria italica</i>)

description: The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including <i>Arabidopsis thaliana</i>, <i>Oryza sativa</i>, and <i>Triticum aestivum</i>, but have not been identified in foxtail millet (<i>Setaria italica</i>). In this study, a total of 93 MAPK cascade genes, including 15 <i>SiMAPKs</i>, 10 <i>SiMAPKKs</i> and 68 <i>SiMAPKKKs</i> genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the <i>SiMAPKs</i> and <i>SiMAPKKs</i> into four subgroups, respectively, and the <i>SiMAPKKKs</i> into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most <i>SiMAPKs</i> and <i>SiMAPKKs</i> were changed under both exogenous hormone and abiotic stress treatments, with <i>SiMAPK3</i> and <i>SiMAPKK4–2</i> being induced under almost all treatments, while the expression of <i>SiMAPKK5</i> was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (<i>Setaria italica</i>).
DOI: 10.6084/m9.figshare.23971690.v1
title: Identification and expression analysis of MAPK cascade gene family in foxtail millet (<i>Setaria italica</i>)

description: The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including <i>Arabidopsis thaliana</i>, <i>Oryza sativa</i>, and <i>Triticum aestivum</i>, but have not been identified in foxtail millet (<i>Setaria italica</i>). In this study, a total of 93 MAPK cascade genes, including 15 <i>SiMAPKs</i>, 10 <i>SiMAPKKs</i> and 68 <i>SiMAPKKKs</i> genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the <i>SiMAPKs</i> and <i>SiMAPKKs</i> into four subgroups, respectively, and the <i>SiMAPKKKs</i> into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most <i>SiMAPKs</i> and <i>SiMAPKKs</i> were changed under both exogenous hormone and abiotic stress treatments, with <i>SiMAPK3</i> and <i>SiMAPKK4–2</i> being induced under almost all treatments, while the expression of <i>SiMAPKK5</i> was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (<i>Setaria italica</i>).
DOI: 10.6084/m9.figshare.21938118
title: Identification and expression analysis of <i>YABBY</i> family genes in <i>Platycodon grandiflorus</i>

description: <i>Platycodon grandiflorus</i> set ornamental, edible, and medicinal plant with broad prospects for further application development. However, there are no reports on the YABBY transcription factor in <i>P. grandiflorus</i>. Identification and analysis of the <i>YABBY</i> gene family of <i>P. grandiflorus</i> using bioinformatics means. Six <i>YABBY</i> genes were identified and divided into five subgroups. Transcriptome data and qRT-PCR were used to analyze the expression patterns of <i>YABBY. YABBY</i> genes exhibited organ-specific patterns in expression in <i>P grandiflorus</i>. Upon salt stress and drought induction, <i>P. grandiflorus</i> presented different morphological and physiological changes with some dynamic changes. Under salt treatment, the <i>YABBY</i> gene family was down-regulated; <i>PgYABBY5</i> was up-regulated in leaves at 24 h. In drought treatment, <i>PgYABBY1, PgYABBY2</i>, and <i>PgYABBY3</i> were down-regulated to varying degrees, but <i>PgYABBY3</i> was significantly up-regulated in the roots. <i>PgYABBY5</i> was up-regulated gradually after being down-regulated. <i>PgYABBY5</i> was significantly up-regulated in stem and leaf at 48 h. <i>PgYABBY6</i> was down-regulated at first and then significantly up-regulated. The dynamic changes of salt stress and drought stress can be regarded as the responses of plants to resist damage. During the whole process of salt and drought stress treatment, the protein content of each tissue part of <i>P grandiflorus</i> changed continuously. At the same time, we found that the promoter region of the <i>PgYABBY</i> gene contains stress-resistant elements, and the regulatory role of YABBY transcription factor in the anti-stress mechanism of <i>P grandiflorus</i> remains to be studied. <i>PgYABBY1, PgYABBY2</i>, and <i>PgYABBY5</i> may be involved in the regulation of saponins in <i>P. grandiflorus. PgYABBY5</i> may be involved in the drought resistance mechanism in <i>P. grandiflorus</i> stems and leaves. This study may provide a theoretical basis for studying the regulation of terpenoids by the YABBY transcription factor and its resistance to abiotic stress.
DOI: 10.6084/m9.figshare.21938118.v1
title: Identification and expression analysis of <i>YABBY</i> family genes in <i>Platycodon grandiflorus</i>

description: <i>Platycodon grandiflorus</i> set ornamental, edible, and medicinal plant with broad prospects for further application development. However, there are no reports on the YABBY transcription factor in <i>P. grandiflorus</i>. Identification and analysis of the <i>YABBY</i> gene family of <i>P. grandiflorus</i> using bioinformatics means. Six <i>YABBY</i> genes were identified and divided into five subgroups. Transcriptome data and qRT-PCR were used to analyze the expression patterns of <i>YABBY. YABBY</i> genes exhibited organ-specific patterns in expression in <i>P grandiflorus</i>. Upon salt stress and drought induction, <i>P. grandiflorus</i> presented different morphological and physiological changes with some dynamic changes. Under salt treatment, the <i>YABBY</i> gene family was down-regulated; <i>PgYABBY5</i> was up-regulated in leaves at 24 h. In drought treatment, <i>PgYABBY1, PgYABBY2</i>, and <i>PgYABBY3</i> were down-regulated to varying degrees, but <i>PgYABBY3</i> was significantly up-regulated in the roots. <i>PgYABBY5</i> was up-regulated gradually after being down-regulated. <i>PgYABBY5</i> was significantly up-regulated in stem and leaf at 48 h. <i>PgYABBY6</i> was down-regulated at first and then significantly up-regulated. The dynamic changes of salt stress and drought stress can be regarded as the responses of plants to resist damage. During the whole process of salt and drought stress treatment, the protein content of each tissue part of <i>P grandiflorus</i> changed continuously. At the same time, we found that the promoter region of the <i>PgYABBY</i> gene contains stress-resistant elements, and the regulatory role of YABBY transcription factor in the anti-stress mechanism of <i>P grandiflorus</i> remains to be studied. <i>PgYABBY1, PgYABBY2</i>, and <i>PgYABBY5</i> may be involved in the regulation of saponins in <i>P. grandiflorus. PgYABBY5</i> may be involved in the drought resistance mechanism in <i>P. grandiflorus</i> stems and leaves. This study may provide a theoretical basis for studying the regulation of terpenoids by the YABBY transcription factor and its resistance to abiotic stress.
DOI: 10.6084/m9.figshare.24763379.v1
title: Trees in trees a report from remote Australia

description: Anemochory or Ornithochory does not adequately explain the amount, size or distribution of woody epiphytes here in outback NSW Australia. In a semi-arid ecosystem, epiphytes should be short-lived and randomly dispersed not clustered around old Aboriginal campsites or along their ancient paths aka songlines. These enduring trees in trees we call TinTs, have been here much longer than European Australians. We are hoping to attract archaeobotanical or ethnobotanical research to help us recover the knowledge of the ancestors or at least assist us in protecting these arboreal oddities from future resource extraction activities.