cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22587711
title: Effect of interfering TOR signaling pathway on the biosynthesis of terpenoids in <i>Salvia miltiorrhiza Bge</i>

description: The TOR (Target of Rapamycin) signaling pathway, which takes TOR kinase as the core, regulates the absorption, distribution, and recycling of nutrients by integrating metabolic network and other signaling pathways, thus participating in the plant growth-defense trade-off. While terpenoids play an important role in plant growth, development, stress response, and signal transduction. The effect of the TOR signaling pathway on terpenoid biosynthesis in plants has yet to be studied in detail. In this study, the tissue culture seedlings of <i>Salvia miltiorrhiza</i> were treated with the TOR inhibitor AZD8055. The results show that the roots of the control group had begun to grow on the 8th day, while the seedlings treated with AZD8055 had no rooting signs. Combined with the expression changes of genes related to the TOR signaling pathway in the first 8 days, samples on the 3rd, 6th, and 8th days were selected for RNA-Seq analysis. Through RNA-Seq analysis, a total of 50,689 unigenes were obtained from the samples of these three periods, of which 4088 unigenes showed differential expression. The function enrichment and time-series analysis of differentially expressed genes (DEGs) showed that the main influence of the TOR signal pathway on plant growth-related processes was gradually transmitted with treatment time after TOR was inhibited. Pathway enrichment analysis of DEGs showed that the genes in the biosynthesis of terpenoids, such as diterpenoid and carotenoid biosynthetic pathways, could be regulated. Compared with other stages, DEGs related to terpenoid biosynthesis were mainly regulated in the S2 stage. In addition, the genes involved in terpenoid skeleton biosynthesis was also considerably enriched in the S2 stage, according to the results of gene set enrichment analysis (GSEA) of unigenes. Inhibition of the TOR signaling pathway may affect the biosynthesis of terpenoid signaling molecules, inhibit gibberellin’s biosynthesis, and promote abscisic acid’s biosynthesis. This study has discussed the effect of interfering with the TOR pathway on terpenoid biosynthesis in <i>S. miltiorrhiza</i> from the perspective of omics and provides new insight into the interaction between the terpenoid biosynthesis pathway and the growth-defense trade-off of medicinal plants.
DOI: 10.6084/m9.figshare.22587711.v1
title: Effect of interfering TOR signaling pathway on the biosynthesis of terpenoids in <i>Salvia miltiorrhiza Bge</i>

description: The TOR (Target of Rapamycin) signaling pathway, which takes TOR kinase as the core, regulates the absorption, distribution, and recycling of nutrients by integrating metabolic network and other signaling pathways, thus participating in the plant growth-defense trade-off. While terpenoids play an important role in plant growth, development, stress response, and signal transduction. The effect of the TOR signaling pathway on terpenoid biosynthesis in plants has yet to be studied in detail. In this study, the tissue culture seedlings of <i>Salvia miltiorrhiza</i> were treated with the TOR inhibitor AZD8055. The results show that the roots of the control group had begun to grow on the 8th day, while the seedlings treated with AZD8055 had no rooting signs. Combined with the expression changes of genes related to the TOR signaling pathway in the first 8 days, samples on the 3rd, 6th, and 8th days were selected for RNA-Seq analysis. Through RNA-Seq analysis, a total of 50,689 unigenes were obtained from the samples of these three periods, of which 4088 unigenes showed differential expression. The function enrichment and time-series analysis of differentially expressed genes (DEGs) showed that the main influence of the TOR signal pathway on plant growth-related processes was gradually transmitted with treatment time after TOR was inhibited. Pathway enrichment analysis of DEGs showed that the genes in the biosynthesis of terpenoids, such as diterpenoid and carotenoid biosynthetic pathways, could be regulated. Compared with other stages, DEGs related to terpenoid biosynthesis were mainly regulated in the S2 stage. In addition, the genes involved in terpenoid skeleton biosynthesis was also considerably enriched in the S2 stage, according to the results of gene set enrichment analysis (GSEA) of unigenes. Inhibition of the TOR signaling pathway may affect the biosynthesis of terpenoid signaling molecules, inhibit gibberellin’s biosynthesis, and promote abscisic acid’s biosynthesis. This study has discussed the effect of interfering with the TOR pathway on terpenoid biosynthesis in <i>S. miltiorrhiza</i> from the perspective of omics and provides new insight into the interaction between the terpenoid biosynthesis pathway and the growth-defense trade-off of medicinal plants.
DOI: 10.6084/m9.figshare.22673388.v1
title: Exogenous Brassinosteroid Enhances Zinc tolerance by activating the Phenylpropanoid Biosynthesis pathway in Citrullus lanatus L

description: Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. The phytohormone brassinosteroids (BRs) play a key role in regulating plant growth, development, and response to stress. However, the role of BRs in watermelon (<i>Citrullus lanatus</i> L.) under Zn stress, one of the most important horticultural crops, remains largely unknown. In this study, we revealed that 24-epibrassinolide (EBR), a bioactive BR enhanced Zn tolerance in watermelon plants, which was related to the EBR-induced increase in the fresh weight, chlorophyll content, and net photosynthetic rate (Pn) and decrease in the content of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), malondialdehyde (MDA), and Zn in watermelon leaves. Through RNA deep sequencing (RNA-seq), 350 different expressed genes (DEG) were found to be involved in the response to Zn stress after EBR treatment, including 175 up-regulated DEGs and 175 down-regulated DEGs. The up-regulated DEGs were significantly enriched in ‘phenylpropanoid biosynthesis’ pathway (map00940) using KEGG enrichment analysis. The gene expression levels of <i>PAL</i>, <i>4CL</i>, <i>CCR</i>, and <i>CCoAOMT</i>, key genes involved in phenylpropanoid pathway, were significantly induced after EBR treatment. In addition, compared with Zn stress alone, EBR treatment significantly promoted the activities of PAL, 4CL, and POD by 30.90%, 20.69%, and 47.28%, respectively, and increased the content of total phenolic compounds, total flavonoids, and lignin by 23.02%, 40.37%, and 29.26%, respectively. The present research indicates that EBR plays an active role in strengthening Zn tolerance, thus providing new insights into the mechanism of BRs enhancing heavy metal tolerance.
DOI: 10.6084/m9.figshare.24463910
title: Expression profiling of the phenylalanine ammonia-lyase (<i>PAL</i>) gene family in <i>ginkgo biloba</i> L.

description: The <i>PAL</i> gene family plays an important role in plant growth, development, and response to abiotic stresses and has been identified in a variety of plants. However, a systematic characterization is still lacking in <i>Ginkgo biloba</i>. Using a bioinformatics approach, 11 <i>GbPAL</i> members of the <i>PAL</i> gene family identified in ginkgo were identified in this study. The protein structure and physicochemical properties indicated that the <i>GbPAL</i> genes were highly similar. Based on their exon-intron structures, they can be classified into three groups. A total of 62 cis-elements for hormone, light, and abiotic stress responses were identified in the promoters of <i>GbPAL</i> genes, indicating that <i>PAL</i> is a multifunctional gene family. <i>GbPAL</i> genes were specifically expressed in different tissues and ploidy of ginkgo. These results provide a theoretical basis for further studies on the functional expression of the <i>GbPAL</i> genes.
DOI: 10.6084/m9.figshare.24463910.v1
title: Expression profiling of the phenylalanine ammonia-lyase (<i>PAL</i>) gene family in <i>ginkgo biloba</i> L.

description: The <i>PAL</i> gene family plays an important role in plant growth, development, and response to abiotic stresses and has been identified in a variety of plants. However, a systematic characterization is still lacking in <i>Ginkgo biloba</i>. Using a bioinformatics approach, 11 <i>GbPAL</i> members of the <i>PAL</i> gene family identified in ginkgo were identified in this study. The protein structure and physicochemical properties indicated that the <i>GbPAL</i> genes were highly similar. Based on their exon-intron structures, they can be classified into three groups. A total of 62 cis-elements for hormone, light, and abiotic stress responses were identified in the promoters of <i>GbPAL</i> genes, indicating that <i>PAL</i> is a multifunctional gene family. <i>GbPAL</i> genes were specifically expressed in different tissues and ploidy of ginkgo. These results provide a theoretical basis for further studies on the functional expression of the <i>GbPAL</i> genes.
DOI: 10.6084/m9.figshare.22673388
title: Exogenous Brassinosteroid Enhances Zinc tolerance by activating the Phenylpropanoid Biosynthesis pathway in Citrullus lanatus L

description: Zinc (Zn) is an important element in plants, but over-accumulation of Zn is harmful. The phytohormone brassinosteroids (BRs) play a key role in regulating plant growth, development, and response to stress. However, the role of BRs in watermelon (<i>Citrullus lanatus</i> L.) under Zn stress, one of the most important horticultural crops, remains largely unknown. In this study, we revealed that 24-epibrassinolide (EBR), a bioactive BR enhanced Zn tolerance in watermelon plants, which was related to the EBR-induced increase in the fresh weight, chlorophyll content, and net photosynthetic rate (Pn) and decrease in the content of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), malondialdehyde (MDA), and Zn in watermelon leaves. Through RNA deep sequencing (RNA-seq), 350 different expressed genes (DEG) were found to be involved in the response to Zn stress after EBR treatment, including 175 up-regulated DEGs and 175 down-regulated DEGs. The up-regulated DEGs were significantly enriched in ‘phenylpropanoid biosynthesis’ pathway (map00940) using KEGG enrichment analysis. The gene expression levels of <i>PAL</i>, <i>4CL</i>, <i>CCR</i>, and <i>CCoAOMT</i>, key genes involved in phenylpropanoid pathway, were significantly induced after EBR treatment. In addition, compared with Zn stress alone, EBR treatment significantly promoted the activities of PAL, 4CL, and POD by 30.90%, 20.69%, and 47.28%, respectively, and increased the content of total phenolic compounds, total flavonoids, and lignin by 23.02%, 40.37%, and 29.26%, respectively. The present research indicates that EBR plays an active role in strengthening Zn tolerance, thus providing new insights into the mechanism of BRs enhancing heavy metal tolerance.
DOI: 10.6084/m9.figshare.24029899
title: Identification, expression analysis of quinoa betalain biosynthesis genes and their role in seed germination and cold stress

description: Betalains provide <i>Chenopodium quinoa</i> bright color, and the key enzyme genes for betalain biosynthesis include <i>CYP76AD</i>, <i>DODA</i>, and <i>GTs</i>. In this study, 59 <i>CqCYP76AD</i>, <i>CqDODA</i> and <i>CqGTs</i> genes in quinoa were identified and characterized by gene structural characteristics, phylogenetic relationships and gene expression patterns. The <i>CqCYP76AD</i> genes were divided into ɑ, β and γ types, <i>CqDODA</i> into ɑ and β types, and <i>CqGTs</i> into <i>CqcDOPA5GT</i>, <i>CqB5GT</i> and <i>CqB6GT</i> types according to phylogenetic relationships. The analysis of co-linearity identified eight pairs of duplicated genes which were subjected to purifying selection during evolution. <i>CqCYP76AD</i> and <i>CqDODA</i>, as well as <i>CqcDOPA5GT</i> and <i>CqB5GT</i> may have been evolutionarily linked in genetic inheritance, based on gene location and gene structure study. The tissue expression specificity of <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in response to seed germination and cold stress was studied by RNA-Seq data. The genes <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> were involved in betalain biosynthesis and cold stress. <i>CqCYP76AD</i>, <i>CqDODA</i>, <i>CqcDOPA5GT</i> and <i>CqB5GT</i> gene sequences were consistent in the eight quinoa samples and showed significant variations in expression. In contrast, the inconsistency between changes in gene expression and betalain accumulation indicates that other factors may influence betalain biosynthesis in quinoa. This study offers the theoretical basis for the roles of the <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in betalain biosynthesis and cold stress in quinoa, as well as a guide for the full utilization of betalains in quinoa plants.
DOI: 10.6084/m9.figshare.24029899.v1
title: Identification, expression analysis of quinoa betalain biosynthesis genes and their role in seed germination and cold stress

description: Betalains provide <i>Chenopodium quinoa</i> bright color, and the key enzyme genes for betalain biosynthesis include <i>CYP76AD</i>, <i>DODA</i>, and <i>GTs</i>. In this study, 59 <i>CqCYP76AD</i>, <i>CqDODA</i> and <i>CqGTs</i> genes in quinoa were identified and characterized by gene structural characteristics, phylogenetic relationships and gene expression patterns. The <i>CqCYP76AD</i> genes were divided into ɑ, β and γ types, <i>CqDODA</i> into ɑ and β types, and <i>CqGTs</i> into <i>CqcDOPA5GT</i>, <i>CqB5GT</i> and <i>CqB6GT</i> types according to phylogenetic relationships. The analysis of co-linearity identified eight pairs of duplicated genes which were subjected to purifying selection during evolution. <i>CqCYP76AD</i> and <i>CqDODA</i>, as well as <i>CqcDOPA5GT</i> and <i>CqB5GT</i> may have been evolutionarily linked in genetic inheritance, based on gene location and gene structure study. The tissue expression specificity of <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in response to seed germination and cold stress was studied by RNA-Seq data. The genes <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> were involved in betalain biosynthesis and cold stress. <i>CqCYP76AD</i>, <i>CqDODA</i>, <i>CqcDOPA5GT</i> and <i>CqB5GT</i> gene sequences were consistent in the eight quinoa samples and showed significant variations in expression. In contrast, the inconsistency between changes in gene expression and betalain accumulation indicates that other factors may influence betalain biosynthesis in quinoa. This study offers the theoretical basis for the roles of the <i>CqCYP76AD</i>, <i>CqDODA</i>, and <i>CqGTs</i> genes in betalain biosynthesis and cold stress in quinoa, as well as a guide for the full utilization of betalains in quinoa plants.
DOI: 10.6084/m9.figshare.24582805
title: Metabolomics analysis of quality components metabolism during the growth process of pepino (<i>Solanum muricatum</i>) fruit

description: Pepino (<i>Solanum muricatum</i>), a horticultural crop that has experienced significant growth in the highlands of China over the past two decades, is widely embraced by consumers due to its distinctive taste and nutritional advantages. This study focused on the cultivar ‘Qingcanxiang’ of pepino grown on the Qinghai-Tibetan Plateau was analyzed using UPLC-QTOF-MS and RNA-seq transcriptome sequencing. Fruit samples were collected at three distinct stages of development, and the results of the metabolomics and transcriptomics were compared and correlated. The study’s findings indicate that the ‘Qingcanxiang’ fruit contained a total of 187 metabolites, comprising 12 distinct categories of compounds, including amino acids and their derivatives, organic acids, sugars and alcohols, phenols and phenolic acids. Of these metabolites, 94 were identified as differential. Significant variations in nutrient composition were observed across the three growth stages of the fruit. Specifically, the stage spanning from the growth to the maturation was identified as the critical stages for nutrient accumulation and flavor development. Transcriptome sequencing analysis revealed a set of highly associated genes between aspartate and quinic acid, namely <i>SIR2</i>, <i>IRAK4</i>, <i>RP-L29</i>, and <i>CCNH</i>. These genes are potentially involved in the regulation of both amino acid and phenolic acid synthesis. Through the application of metabolomics and transcriptomics, this investigation elucidates the alterations in metabolites and the underlying molecular regulatory mechanisms of pepino fruits during three growth stages. The findings furnish a theoretical foundation for the evaluation of nutritional quality and the enhancement of breeding strategies for pepino.
DOI: 10.6084/m9.figshare.24582805.v1
title: Metabolomics analysis of quality components metabolism during the growth process of pepino (<i>Solanum muricatum</i>) fruit

description: Pepino (<i>Solanum muricatum</i>), a horticultural crop that has experienced significant growth in the highlands of China over the past two decades, is widely embraced by consumers due to its distinctive taste and nutritional advantages. This study focused on the cultivar ‘Qingcanxiang’ of pepino grown on the Qinghai-Tibetan Plateau was analyzed using UPLC-QTOF-MS and RNA-seq transcriptome sequencing. Fruit samples were collected at three distinct stages of development, and the results of the metabolomics and transcriptomics were compared and correlated. The study’s findings indicate that the ‘Qingcanxiang’ fruit contained a total of 187 metabolites, comprising 12 distinct categories of compounds, including amino acids and their derivatives, organic acids, sugars and alcohols, phenols and phenolic acids. Of these metabolites, 94 were identified as differential. Significant variations in nutrient composition were observed across the three growth stages of the fruit. Specifically, the stage spanning from the growth to the maturation was identified as the critical stages for nutrient accumulation and flavor development. Transcriptome sequencing analysis revealed a set of highly associated genes between aspartate and quinic acid, namely <i>SIR2</i>, <i>IRAK4</i>, <i>RP-L29</i>, and <i>CCNH</i>. These genes are potentially involved in the regulation of both amino acid and phenolic acid synthesis. Through the application of metabolomics and transcriptomics, this investigation elucidates the alterations in metabolites and the underlying molecular regulatory mechanisms of pepino fruits during three growth stages. The findings furnish a theoretical foundation for the evaluation of nutritional quality and the enhancement of breeding strategies for pepino.
DOI: 10.6084/m9.figshare.23244388
title: Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn

description: Yellow horn grows in northern China and has a high tolerance to drought and poor soil. Improving photosynthetic efficiency and increasing plant growth and yield under drought conditions have become important research content for researchers worldwide. Our study goal is to provide comprehensive information on photosynthesis and some candidate genes breeding of yellow horn under drought stress. In this study, seedlings’ stomatal conductance, chlorophyll content, and fluorescence parameters decreased under drought stress, but non-photochemical quenching increased. The leaf microstructure showed that stomata underwent a process from opening to closing, guard cells from complete to dry, and surrounding leaf cells from smooth to severe shrinkage. The chloroplast ultrastructure showed that the changes of starch granules were different under different drought stress, while plastoglobules increased and expanded continuously. In addition, we found some differentially expressed genes related to photosystem, electron transport component, oxidative phosphate ATPase, stomatal closure, and chloroplast ultrastructure. These results laid a foundation for further genetic improvement and deficit resistance breeding of yellow horn under drought stress.
DOI: 10.6084/m9.figshare.23244388.v1
title: Effects of drought stress on photosynthetic physiological characteristics, leaf microstructure, and related gene expression of yellow horn

description: Yellow horn grows in northern China and has a high tolerance to drought and poor soil. Improving photosynthetic efficiency and increasing plant growth and yield under drought conditions have become important research content for researchers worldwide. Our study goal is to provide comprehensive information on photosynthesis and some candidate genes breeding of yellow horn under drought stress. In this study, seedlings’ stomatal conductance, chlorophyll content, and fluorescence parameters decreased under drought stress, but non-photochemical quenching increased. The leaf microstructure showed that stomata underwent a process from opening to closing, guard cells from complete to dry, and surrounding leaf cells from smooth to severe shrinkage. The chloroplast ultrastructure showed that the changes of starch granules were different under different drought stress, while plastoglobules increased and expanded continuously. In addition, we found some differentially expressed genes related to photosystem, electron transport component, oxidative phosphate ATPase, stomatal closure, and chloroplast ultrastructure. These results laid a foundation for further genetic improvement and deficit resistance breeding of yellow horn under drought stress.
DOI: 10.6084/m9.figshare.24198503
title: Phosphorylation-mediated regulation of integrin-linked kinase 5 by purinoreceptor P2K2

description: Extracellular ATP (eATP) in plants plays a crucial role as a ligand for purinoreceptors, mediating purinergic signaling and regulating diverse biological functions, including responses to abiotic and biotic stresses. DORN1/P2K1 (LecRK I.9) was the first identified plant purinoreceptor. P2K2 (LecRK I.5) was subsequently identified as an additional plant purinoreceptor and shown to directly interact with P2K1. Recently, we reported that P2K1 interacts with Integrin-linked kinase 5 (ILK5), a Raf-like MAPKKK protein, and phosphorylates ILK5 to regulate purinergic signaling in relation to plant innate immunity. Here, we report that P2K2 also interacts with the ILK5 protein <i>in planta</i>. Furthermore, we demonstrate that P2K2 phosphorylates ILK5 in the presence of [γ-32P] ATP, similar to P2K1. However, unlike P2K1, P2K2 exhibits strong phosphorylation even when the Serine 192 residue of ILK5 is mutated to Alanine (ILK5<sup>S192A</sup>), suggesting the possibility of phosphorylation of other residues to fully regulate ILK5 protein function.
DOI: 10.6084/m9.figshare.24198503.v1
title: Phosphorylation-mediated regulation of integrin-linked kinase 5 by purinoreceptor P2K2

description: Extracellular ATP (eATP) in plants plays a crucial role as a ligand for purinoreceptors, mediating purinergic signaling and regulating diverse biological functions, including responses to abiotic and biotic stresses. DORN1/P2K1 (LecRK I.9) was the first identified plant purinoreceptor. P2K2 (LecRK I.5) was subsequently identified as an additional plant purinoreceptor and shown to directly interact with P2K1. Recently, we reported that P2K1 interacts with Integrin-linked kinase 5 (ILK5), a Raf-like MAPKKK protein, and phosphorylates ILK5 to regulate purinergic signaling in relation to plant innate immunity. Here, we report that P2K2 also interacts with the ILK5 protein <i>in planta</i>. Furthermore, we demonstrate that P2K2 phosphorylates ILK5 in the presence of [γ-32P] ATP, similar to P2K1. However, unlike P2K1, P2K2 exhibits strong phosphorylation even when the Serine 192 residue of ILK5 is mutated to Alanine (ILK5<sup>S192A</sup>), suggesting the possibility of phosphorylation of other residues to fully regulate ILK5 protein function.