cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26539235
title: Requirement of two simultaneous environmental signals for activation of Arabidopsis <i>ELIP2</i> promoter in response to high light, cold, and UV-B stresses

description: Arabidopsis EARLY LIGH-INDUCIBLE PROTEIN 2 (ELIP2) is a chlorophyll- and carotenoid-binding protein and is involved in photoprotection under stress conditions. Because its expression is induced through high light, cold, or UV-B stressors, its mechanism of induction has been studied. It is known that a functional unit found in the promoter, which is composed of Element B and Element A, is required and sufficient for full activation by these stressors. In this study, the role of each element in the unit was analyzed by introducing weak mutations in each element as synthetic promoters in addition to intensive repeat constructs of each single element. The results suggest that a stressor like cold stress generates two parallel signals in plant cells, and they merge at the promoter region for the activation of <i>ELIP2</i> expression, which constitutes an “AND” gate and has a potential to realize strong response with high specificity by an environmental trigger.
DOI: 10.6084/m9.figshare.27997828
title: Growth and physiological response of Yulu <i>Hippophae rhamnoides</i> to drought stress and its omics analysis

description: <i>Hippophae rhamnoides (H. rhamnoides</i>) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of <i>H. rhamnoides</i> roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu <i>H. rhamnoides</i> was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu <i>H. rhamnoides</i> may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of <i>H. rhamnoides</i> were discussed in greater detail.
DOI: 10.6084/m9.figshare.27997828.v1
title: Growth and physiological response of Yulu <i>Hippophae rhamnoides</i> to drought stress and its omics analysis

description: <i>Hippophae rhamnoides (H. rhamnoides</i>) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of <i>H. rhamnoides</i> roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu <i>H. rhamnoides</i> was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu <i>H. rhamnoides</i> may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of <i>H. rhamnoides</i> were discussed in greater detail.
DOI: 10.6084/m9.figshare.26107997
title: Drought-induced molecular changes in crown of various barley phytohormone mutants

description: One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the <i>hvdwarf14.d</i> mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the <i>HvGA20ox2</i>, <i>HvBRI1</i>, and <i>HvD14</i> genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and <i>vice versa</i>, but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.
DOI: 10.6084/m9.figshare.26107997.v1
title: Drought-induced molecular changes in crown of various barley phytohormone mutants

description: One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the <i>hvdwarf14.d</i> mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the <i>HvGA20ox2</i>, <i>HvBRI1</i>, and <i>HvD14</i> genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and <i>vice versa</i>, but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.
DOI: 10.6084/m9.figshare.26543568
title: Decoding the role of <i>OsPRX83</i> in enhancing osmotic stress tolerance in rice through ABA-dependent pathways and ROS scavenging

description: Plant Class III peroxidases have diverse roles in controlling root hair growth, anther development, and abiotic and biotic stress responses. However, their abiotic stress response mechanism in rice remains elusive. Here, we identified a peroxidase precursor gene, <i>OsPRX83</i>, and investigated its role in enhancing osmotic stress tolerance in rice. We used <i>OsPRX83</i> overexpression and CRISPR-Cas9-generated mutant lines to elucidate <i>OsPRX83</i>‘s function and expression patterns under stress conditions. The expression of <i>OsPRX83</i> was induced by H<sub>2</sub>O<sub>2</sub>, PEG, NaCl, and ABA treatments. Using qRT-PCR, RNA sequencing, and physiological assays, we demonstrated that overexpression of <i>OsPRX83</i> enhanced the osmotic and oxidative stress tolerance as compared to the wild-type and mutant seedlings, as evident from the higher survival rates, enhanced peroxidase (POD) and ascorbate peroxidase (APX) activities, and increased ABA sensitivity compared with mutants and wild-type plants. Transcriptome analysis further supported the involvement of <i>OsPRX83</i> in the ROS scavenging, by modulating the expression of <i>OsDREB1B</i>, <i>OsDREB1E</i>, <i>OsDREB1F</i>, <i>OsDREB1G</i> in response to osmotic treatment. In summary, our study suggests that <i>OsPRX83</i> plays a pivotal role in enhancing stress tolerance in rice through ABA-dependent pathways and ROS scavenging. Therefore, this study elucidates the function of a novel abiotic stress response gene in rice, thereby may contribute to a new genetic engineering resource for engineering drought-resistant rice varieties.
DOI: 10.6084/m9.figshare.26543568.v1
title: Decoding the role of <i>OsPRX83</i> in enhancing osmotic stress tolerance in rice through ABA-dependent pathways and ROS scavenging

description: Plant Class III peroxidases have diverse roles in controlling root hair growth, anther development, and abiotic and biotic stress responses. However, their abiotic stress response mechanism in rice remains elusive. Here, we identified a peroxidase precursor gene, <i>OsPRX83</i>, and investigated its role in enhancing osmotic stress tolerance in rice. We used <i>OsPRX83</i> overexpression and CRISPR-Cas9-generated mutant lines to elucidate <i>OsPRX83</i>‘s function and expression patterns under stress conditions. The expression of <i>OsPRX83</i> was induced by H<sub>2</sub>O<sub>2</sub>, PEG, NaCl, and ABA treatments. Using qRT-PCR, RNA sequencing, and physiological assays, we demonstrated that overexpression of <i>OsPRX83</i> enhanced the osmotic and oxidative stress tolerance as compared to the wild-type and mutant seedlings, as evident from the higher survival rates, enhanced peroxidase (POD) and ascorbate peroxidase (APX) activities, and increased ABA sensitivity compared with mutants and wild-type plants. Transcriptome analysis further supported the involvement of <i>OsPRX83</i> in the ROS scavenging, by modulating the expression of <i>OsDREB1B</i>, <i>OsDREB1E</i>, <i>OsDREB1F</i>, <i>OsDREB1G</i> in response to osmotic treatment. In summary, our study suggests that <i>OsPRX83</i> plays a pivotal role in enhancing stress tolerance in rice through ABA-dependent pathways and ROS scavenging. Therefore, this study elucidates the function of a novel abiotic stress response gene in rice, thereby may contribute to a new genetic engineering resource for engineering drought-resistant rice varieties.
DOI: 10.6084/m9.figshare.25450392
title: Physiological and transcriptomic analysis of tomato in response to sub-optimal temperature stress

description: Tomato (<i>Solanum lycopersicum</i> L.) is one of the most important economic crops in China. However, its quality and yield are susceptible to the adverse effects of low temperatures. In our study, two tomato cultivars, showing different tolerance to low temperatures, namely the cold-sensitive tomato cultivar (S708) and cold-tolerant tomato cultivar (T722), were grown at optimal (25/18°C) and sub-optimal (15/10°C) temperature conditions for 5 days. Our study aimed to explore the effect of sub-optimal temperature on fresh weight, chlorophyll content and chlorophyll fluorescence, soluble sugars and proline content of two tomato cultivars. Moreover, we employed RNA-Seq to analyze the transcriptomic response of tomato roots to sub-optimal temperature. The results revealed that S708 showed a more significant reduction in fresh weight, chlorophyll content, photochemical efficiency of PSII (YII), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qP) and electron transport rate (ETR) compared to T722 under the sub-optimal temperature condition. Notably, T722 maintained higher level of soluble sugars and proline in comparison to S708 uner sub-optimal temperature. RNA-seq data showed that up-regulated DEGs in both tomato cultivars were involved in “plant-pathogen interaction”, “MAPK signaling pathway”, “plant hormone signal transduction”, and “phosphatidylinositol signaling system”. Furthermore, “Amino sugar and nucleotide sugar metabolism” pathway was enriched only in T722. Moreover, under sub-optimal temperature, transcription factor genes and osmoregulation genes showed varying degrees of response in both tomato cultivars. Conclusion: In summary, our results offer detailed insights into the response characteristics of tomato to sub-optimal temperature, providing valuable references for the practical management of tomato crops under sub-optimal temperature condition.
DOI: 10.6084/m9.figshare.25450392.v1
title: Physiological and transcriptomic analysis of tomato in response to sub-optimal temperature stress

description: Tomato (<i>Solanum lycopersicum</i> L.) is one of the most important economic crops in China. However, its quality and yield are susceptible to the adverse effects of low temperatures. In our study, two tomato cultivars, showing different tolerance to low temperatures, namely the cold-sensitive tomato cultivar (S708) and cold-tolerant tomato cultivar (T722), were grown at optimal (25/18°C) and sub-optimal (15/10°C) temperature conditions for 5 days. Our study aimed to explore the effect of sub-optimal temperature on fresh weight, chlorophyll content and chlorophyll fluorescence, soluble sugars and proline content of two tomato cultivars. Moreover, we employed RNA-Seq to analyze the transcriptomic response of tomato roots to sub-optimal temperature. The results revealed that S708 showed a more significant reduction in fresh weight, chlorophyll content, photochemical efficiency of PSII (YII), maximum quantum yield of PSII (Fv/Fm), photochemical quenching (qP) and electron transport rate (ETR) compared to T722 under the sub-optimal temperature condition. Notably, T722 maintained higher level of soluble sugars and proline in comparison to S708 uner sub-optimal temperature. RNA-seq data showed that up-regulated DEGs in both tomato cultivars were involved in “plant-pathogen interaction”, “MAPK signaling pathway”, “plant hormone signal transduction”, and “phosphatidylinositol signaling system”. Furthermore, “Amino sugar and nucleotide sugar metabolism” pathway was enriched only in T722. Moreover, under sub-optimal temperature, transcription factor genes and osmoregulation genes showed varying degrees of response in both tomato cultivars. Conclusion: In summary, our results offer detailed insights into the response characteristics of tomato to sub-optimal temperature, providing valuable references for the practical management of tomato crops under sub-optimal temperature condition.
DOI: 10.6084/m9.figshare.26939835
title: Characteristics and functions of volatile organic compounds in the tripartite symbiotic system of <i>Gastrodia elata-Armillaria gallica-Rahnella aceris</i> HPDA25

description: Tripartite interactions among plants, fungi, and bacteria are critical for maintaining plant growth and fitness, and volatile organic compounds (VOCs) play a significant role in these interactions. However, the functions of VOCs within the niche of mycoheterotrophic plants, which represent unique types of interactions, remain poorly understood. <i>Gastrodia elata</i>, a mycoheterotrophic orchid species, forms a symbiotic relationship with specific <i>Armillaria</i> species, serving as a model system to investigate this intriguing issue. <i>Rahnella aceris</i> HPDA25 is a plant growth-promoting bacteria isolated from <i>G. elata</i>, which has been found to facilitate the establishment of <i>G. elata-Armillaria</i> symbiosis. In this study, using the tripartite symbiotic system of <i>G. elata-Armillaria gallica-R. aceris</i> HPDA25, we investigate the role of VOCs in the interaction among mycoheterotrophic plants, fungi, and bacteria. Our results showed that 33 VOCs of HPDA25-inducible symbiotic <i>G. elata</i> elevated compared to non-symbiotic <i>G. elata</i>, indicating that VOCs indeed play a role in the symbiotic process. Among these, 21 VOCs were accessible, and six active VOCs showed complete growth inhibition activities against <i>A. gallica</i>, while <i>R. aceris</i> HPDA25 had no significant effect. In addition, three key genes of <i>G. elata</i> have been identified that may contribute to the increased concentration of six active VOCs. These results revealed for the first time the VOCs profile of <i>G. elata</i> and demonstrated its regulatory role in the tripartite symbiotic system involving <i>G. elata</i>, <i>Armillaria</i>, and bacteria.
DOI: 10.6084/m9.figshare.26939835.v1
title: Characteristics and functions of volatile organic compounds in the tripartite symbiotic system of <i>Gastrodia elata-Armillaria gallica-Rahnella aceris</i> HPDA25

description: Tripartite interactions among plants, fungi, and bacteria are critical for maintaining plant growth and fitness, and volatile organic compounds (VOCs) play a significant role in these interactions. However, the functions of VOCs within the niche of mycoheterotrophic plants, which represent unique types of interactions, remain poorly understood. <i>Gastrodia elata</i>, a mycoheterotrophic orchid species, forms a symbiotic relationship with specific <i>Armillaria</i> species, serving as a model system to investigate this intriguing issue. <i>Rahnella aceris</i> HPDA25 is a plant growth-promoting bacteria isolated from <i>G. elata</i>, which has been found to facilitate the establishment of <i>G. elata-Armillaria</i> symbiosis. In this study, using the tripartite symbiotic system of <i>G. elata-Armillaria gallica-R. aceris</i> HPDA25, we investigate the role of VOCs in the interaction among mycoheterotrophic plants, fungi, and bacteria. Our results showed that 33 VOCs of HPDA25-inducible symbiotic <i>G. elata</i> elevated compared to non-symbiotic <i>G. elata</i>, indicating that VOCs indeed play a role in the symbiotic process. Among these, 21 VOCs were accessible, and six active VOCs showed complete growth inhibition activities against <i>A. gallica</i>, while <i>R. aceris</i> HPDA25 had no significant effect. In addition, three key genes of <i>G. elata</i> have been identified that may contribute to the increased concentration of six active VOCs. These results revealed for the first time the VOCs profile of <i>G. elata</i> and demonstrated its regulatory role in the tripartite symbiotic system involving <i>G. elata</i>, <i>Armillaria</i>, and bacteria.
DOI: 10.6084/m9.figshare.26723044
title: MAPK3-MYB36-ARF1 module regulates the tanshinone formation in <i>Salvia miltiorrhiza</i>

description: <i>Salvia miltiorrhiza</i>, known as Danshen, is a traditional Chinese medicinal plant with significant cardiovascular benefits, attributed to its secondary metabolites, particularly tanshinones. Despite their medicinal value, tanshinones occur in low natural abundance, necessitating research to increase their content. This study explores the role of the ARF transcription factor (SmARF1) in tanshinone accumulation in Danshen. Overexpressing <i>SmARF1</i> in hairy roots significantly increased tanshinone levels. EMSA and Dual-LUC assays revealed that SmMYB36, a transcription factor interacting with SmMAPK3, binds to and regulates the <i>SmARF1</i> promoter. SmMYB36 alone inhibited the expression of <i>SmARF1</i> gene, while its interaction with SmMAPK3 enhanced <i>SmARF1</i> promoter activity. This MAPK3-MYB36-ARF1 module elucidates a complex regulatory mechanism for tanshinone biosynthesis, offering insights for targeted enhancement of tanshinone content through advanced biotechnological approaches.