cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21443985
title: Comparison analysis of metabolite profiling in seeds and bark of <i>Ulmus parvifolia</i>, a Chinese medicine species

description: <i>Ulmus parvifolia</i> (<i>U. parvifolia</i>) is a Chinese medicine plant whose bark and leaves are used in the treatment of some diseases such as inflammation, diarrhea and fever. However, metabolic signatures of seeds have not been studied. The seeds and bark of <i>U. parvifolia</i> collected at the seed ripening stage were used for metabolite profiling analysis through the untargeted metabolomics approach. A total of 2,578 and 2,207 metabolites, while 503 and 132 unique metabolites were identified in seeds and bark, respectively. Additionally, 574 differential metabolites (DEMs) were detected in the two different organs of <i>U. parvifolia</i>, which were grouped into 52 classes. Most kinds of metabolites classed into prenol lipids class. The relative content of flavonoids class was the highest. DEMs contained some bioactive compounds (e.g., flavonoids, terpene glycosides, triterpenoids, sesquiterpenoids) with antioxidant, anti-inflammatory, and anti-cancer activities. Most kinds of flavonoids and sesquiterpenes were up-regulated in seeds. There were more varieties of terpene glycosides and triterpenoids showing up-regulated in bark. The pathway enrichment was performed, while flavonoid biosynthesis, flavone and flavonol biosynthesis were worthy of attention. This study identified DEMs with pharmaceutical value between seeds and bark during seed maturation and offered a molecular basis for alternative or complementary use of seeds and bark of <i>U. parvifolia</i> as a Chinese medicinal material.
DOI: 10.6084/m9.figshare.21443985.v1
title: Comparison analysis of metabolite profiling in seeds and bark of <i>Ulmus parvifolia</i>, a Chinese medicine species

description: <i>Ulmus parvifolia</i> (<i>U. parvifolia</i>) is a Chinese medicine plant whose bark and leaves are used in the treatment of some diseases such as inflammation, diarrhea and fever. However, metabolic signatures of seeds have not been studied. The seeds and bark of <i>U. parvifolia</i> collected at the seed ripening stage were used for metabolite profiling analysis through the untargeted metabolomics approach. A total of 2,578 and 2,207 metabolites, while 503 and 132 unique metabolites were identified in seeds and bark, respectively. Additionally, 574 differential metabolites (DEMs) were detected in the two different organs of <i>U. parvifolia</i>, which were grouped into 52 classes. Most kinds of metabolites classed into prenol lipids class. The relative content of flavonoids class was the highest. DEMs contained some bioactive compounds (e.g., flavonoids, terpene glycosides, triterpenoids, sesquiterpenoids) with antioxidant, anti-inflammatory, and anti-cancer activities. Most kinds of flavonoids and sesquiterpenes were up-regulated in seeds. There were more varieties of terpene glycosides and triterpenoids showing up-regulated in bark. The pathway enrichment was performed, while flavonoid biosynthesis, flavone and flavonol biosynthesis were worthy of attention. This study identified DEMs with pharmaceutical value between seeds and bark during seed maturation and offered a molecular basis for alternative or complementary use of seeds and bark of <i>U. parvifolia</i> as a Chinese medicinal material.
DOI: 10.6084/m9.figshare.20117448
title: Genome-wide identification and expression analysis of the NAC transcription factor family in <i>Saccharum spontaneum</i> under different stresses

description: The <i>NAC</i> (<i>NAM, ATAF1/2</i>, and <i>CUC2</i>) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The <i>NAC</i> family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the <i>NAC</i> gene family in the wild species <i>Saccharum spontaneum</i> has not been systematically studied. In this study, 115 <i>SsNAC</i> genes were identified in the <i>S. spontaneum</i> genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the <i>SsNAC</i> family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The <i>SsNAC</i> gene has different expression patterns at different developmental stages of stems and leaves. Further qRT–PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 <i>SsNAC</i> genes, indicating that these genes may play a key role in the resistance of <i>S. spontaneum</i> to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the <i>NAC</i> transcription factor family, providing a reference for further functional studies of the <i>SsNAC</i> gene.
DOI: 10.6084/m9.figshare.19947817
title: Genome-wide identification and expression analysis of <i>DREB</i> genes in alfalfa (<i>Medicago sativa</i>) in response to cold stress

description: Dehydration-responsive element-binding proteins (DREBs) belong to members of the AP2/ERF transcription factor superfamily, which has been reported to involve various abiotic-stress responses and tolerance in plants. However, research on the <i>DREB</i>-family is still limited in alfalfa (<i>Medicago sativa</i> L.), a forage legume cultivated worldwide. The recent genome-sequence release of the alfalfa cultivar “XinJiangDaYe” allowed us to identify 172 <i>DREBs</i> by a multi-step homolog search. The phylogenetic analysis indicated that such <i>MsDREB</i>s could be classified into 5 groups, namely A-1 (56 members), A-2 (39), A-3 (3), A-4 (61) and 13 (A-5 (13), thus adding substantial new members to the <i>DREB</i>-family in alfalfa. Furthermore, a comprehensive survey in <i>silico</i> of conserved motif, gene structure, molecular weight, and isoelectric point (pI) as well as gene expression was conducted. The resulting data showed that, for cold-stress response, 33 differentially expressed <i>MsDREB</i>s were identified with a threshold of Log2-fold &gt; 1, and most of which were transcriptionally upregulated within 48 h during a cold treatment(s). Moreover, the expression profiling of <i>MsDREB</i>s from two ecotypes of alfalfa subspecies i.e. <i>M. sativa</i> ssp. <i>falcata</i> (F56, from a colder region of Central Asia) and <i>M. sativa</i> ssp. <i>sativa</i> (B47, from Near East) revealed that most of the cold-stress responsive <i>MsDREBs</i> exhibited a significantly lower expression in F56, leading to a proposal of the existence of a distinct mechanism(s) for cold tolerance regulated by DREB-related action, which would have been evolved in alfalfa with a genotypic specificity. Additionally, by examining the transcriptome of a freezing-tolerance species (<i>M. sativa</i> cv. Zhaodong), eight <i>DREBs</i> were found to be implicated in a long-term freezing-stress adaptation with a great potential. Taken together, the current genome-wide identification in alfalfa points to the importance of some <i>MsDREB</i>s in the cold-stress response, providing some promising molecular targets to be functionally characterized for the improvement of cold tolerance in crops including alfalfa.
DOI: 10.6084/m9.figshare.19947817.v2
title: Genome-wide identification and expression analysis of <i>DREB</i> genes in alfalfa (<i>Medicago sativa</i>) in response to cold stress

description: Dehydration-responsive element-binding proteins (DREBs) belong to members of the AP2/ERF transcription factor superfamily, which has been reported to involve various abiotic-stress responses and tolerance in plants. However, research on the <i>DREB</i>-family is still limited in alfalfa (<i>Medicago sativa</i> L.), a forage legume cultivated worldwide. The recent genome-sequence release of the alfalfa cultivar “XinJiangDaYe” allowed us to identify 172 <i>DREBs</i> by a multi-step homolog search. The phylogenetic analysis indicated that such <i>MsDREB</i>s could be classified into 5 groups, namely A-1 (56 members), A-2 (39), A-3 (3), A-4 (61) and 13 (A-5 (13), thus adding substantial new members to the <i>DREB</i>-family in alfalfa. Furthermore, a comprehensive survey in <i>silico</i> of conserved motif, gene structure, molecular weight, and isoelectric point (pI) as well as gene expression was conducted. The resulting data showed that, for cold-stress response, 33 differentially expressed <i>MsDREB</i>s were identified with a threshold of Log2-fold &gt; 1, and most of which were transcriptionally upregulated within 48 h during a cold treatment(s). Moreover, the expression profiling of <i>MsDREB</i>s from two ecotypes of alfalfa subspecies i.e. <i>M. sativa</i> ssp. <i>falcata</i> (F56, from a colder region of Central Asia) and <i>M. sativa</i> ssp. <i>sativa</i> (B47, from Near East) revealed that most of the cold-stress responsive <i>MsDREBs</i> exhibited a significantly lower expression in F56, leading to a proposal of the existence of a distinct mechanism(s) for cold tolerance regulated by DREB-related action, which would have been evolved in alfalfa with a genotypic specificity. Additionally, by examining the transcriptome of a freezing-tolerance species (<i>M. sativa</i> cv. Zhaodong), eight <i>DREBs</i> were found to be implicated in a long-term freezing-stress adaptation with a great potential. Taken together, the current genome-wide identification in alfalfa points to the importance of some <i>MsDREB</i>s in the cold-stress response, providing some promising molecular targets to be functionally characterized for the improvement of cold tolerance in crops including alfalfa.
DOI: 10.6084/m9.figshare.20117938
title: Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in <i>Platycodon grandiflorus</i>

description: <i>Platycodon grandiflorus</i>, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of <i>P. grandiflorus</i> are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in <i>P. grandiflorus</i>. In this study, 27 PgWRKYs were identified in the <i>P. grandiflorus</i> transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.
DOI: 10.6084/m9.figshare.20117938.v1
title: Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in <i>Platycodon grandiflorus</i>

description: <i>Platycodon grandiflorus</i>, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of <i>P. grandiflorus</i> are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in <i>P. grandiflorus</i>. In this study, 27 PgWRKYs were identified in the <i>P. grandiflorus</i> transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.
DOI: 10.6084/m9.figshare.18515110
title: A DEK domain-containing protein GhDEK2D mediated <i>Gossypium hirsutum</i> enhanced resistance to <i>Verticillium dahliae</i>

description: DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, <i>GhDEK</i>2D was identified in <i>Gossypium hirsutum</i> by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under <i>Verticillium dahliae</i> (<i>Vd</i>) challenge. The <i>GhDEK2D</i>-silenced cotton decreased resistance against <i>Vd</i>. In <i>GhDEK2D</i>-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic <i>Arabidopsis</i> lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
DOI: 10.6084/m9.figshare.18515110.v1
title: A DEK domain-containing protein GhDEK2D mediated <i>Gossypium hirsutum</i> enhanced resistance to <i>Verticillium dahliae</i>

description: DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, <i>GhDEK</i>2D was identified in <i>Gossypium hirsutum</i> by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under <i>Verticillium dahliae</i> (<i>Vd</i>) challenge. The <i>GhDEK2D</i>-silenced cotton decreased resistance against <i>Vd</i>. In <i>GhDEK2D</i>-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic <i>Arabidopsis</i> lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
DOI: 10.6084/m9.figshare.19713740
title: A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism

description: The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.
DOI: 10.6084/m9.figshare.19713740.v1
title: A conserved oxalyl-coenzyme A decarboxylase in oxalate catabolism

description: The ability to biosynthesize oxalic acid can provide beneficial functions to plants; however, uncontrolled or prolonged exposure to this strong organic acid results in multiple physiological problems. Such problems include a disruption of membrane integrity, mitochondrial function, metal chelation, and free radical formation. Recent work suggests that a CoA-dependent pathway of oxalate catabolism plays a critical role in regulating tissue oxalate concentrations in plants. Although this CoA-dependent pathway of oxalate catabolism is important, large gaps in our knowledge of the enzymes catalyzing each step remain. Evidence that an oxalyl-CoA decarboxylase (OXC) catalyzes the second step in this pathway, accelerating the conversion of oxalyl-CoA to formyl-CoA, has been reported. Induction studies revealed that OXC gene expression was upregulated in response to an exogenous oxalate supply. Phylogenetic analysis indicates that OXCs are conserved across plant species. Evolutionarily the plant OXCs can be separated into dicot and monocot classes. Multiple sequence alignments and molecular modeling suggest that OXCs have similar functionality with three conserved domains, the N-terminal PYR domain, the middle R domain, and the C-terminal PP domain. Further study of this CoA-dependent pathway of oxalate degradation would benefit efforts to develop new strategies to improve the nutrition quality of crops.
DOI: 10.6084/m9.figshare.20526760
title: Strigol induces germination of the facultative parasitic plant <i>Phtheirospermum japonicum</i> in the absence of nitrate ions

description: Root parasitic plants in the family Orobanchaceae, such as <i>Striga</i> and <i>Orobanche</i> spp., infest major crops worldwide, leading to a multibillion-dollar loss annually. Host-derived strigolactones (SLs), recognized by a group of α/β hydrolase receptors (KAI2d) in these parasites, are important determinants for germinating root parasitic plants near the roots of host plants. <i>Phtheirospermum japonicum</i>, a facultative hemiparasitic Orobanchaceae plant, can germinate and grow in the presence or absence of the host and can also exhibit root chemotropism to host-derived SLs that are perceived via KAI2d. However, the importance of SLs in <i>P. japonicum</i> germination remains unclear. In this study, we found that germination of <i>P. japonicum</i> was suppressed in the absence of nitrate ions and that germination of <i>P. japonicum</i> was promoted by exogenous strigol, an SL, under such conditions. We propose a model in which <i>P. japonicum</i> may select either independent living or parasitism in response to ambient nitrogen conditions and host presence.
DOI: 10.6084/m9.figshare.20526760.v1
title: Strigol induces germination of the facultative parasitic plant <i>Phtheirospermum japonicum</i> in the absence of nitrate ions

description: Root parasitic plants in the family Orobanchaceae, such as <i>Striga</i> and <i>Orobanche</i> spp., infest major crops worldwide, leading to a multibillion-dollar loss annually. Host-derived strigolactones (SLs), recognized by a group of α/β hydrolase receptors (KAI2d) in these parasites, are important determinants for germinating root parasitic plants near the roots of host plants. <i>Phtheirospermum japonicum</i>, a facultative hemiparasitic Orobanchaceae plant, can germinate and grow in the presence or absence of the host and can also exhibit root chemotropism to host-derived SLs that are perceived via KAI2d. However, the importance of SLs in <i>P. japonicum</i> germination remains unclear. In this study, we found that germination of <i>P. japonicum</i> was suppressed in the absence of nitrate ions and that germination of <i>P. japonicum</i> was promoted by exogenous strigol, an SL, under such conditions. We propose a model in which <i>P. japonicum</i> may select either independent living or parasitism in response to ambient nitrogen conditions and host presence.
DOI: 10.6084/m9.figshare.21541393
title: A novel type of phytosulfokine, PSK-ε, positively regulates root elongation and formation of lateral roots and root nodules in <i>Medicago truncatula</i>

description: Phytosulfokines (PSKs) are a class of tyrosine-sulfated pentapeptides. PSK-α, PSK-γ, and PSK-δ are three reported PSK members involved in regulating plant growth, development, and resistance to biotic and abiotic stresses. Here, we reported a novel type of PSK, PSK-ε with the sequence Y<sub>SO3</sub>VY<sub>SO3</sub>TN, and its precursor proteins (MtPSKε, LjPSKε, and GmPSKε), specifically from legume species. PSK-ε peptide differs from PSK-δ by one amino acid and is close to PSK-δ in the phylogenetic relationship. Expression profile analysis showed that <i>MtPSKε</i> was highly expressed in <i>Medicago truncatula</i> roots, especially in root tips and emerged lateral roots. Application of the synthetic sulfated PSK-ε peptide and overexpression of <i>MtPSKε</i> significantly promoted <i>M. truncatula</i> root elongation and increased lateral root number, probably by inducing cell division and expansion in roots. Furthermore, <i>MtPSKε</i> expression was induced by rhizobia infection and was detected in root nodules including nodule primordia. Both PSK-ε peptide treatment and <i>MtPSKε</i> overexpression significantly increased nodule number in <i>M. truncatula</i>. Taken together, these results demonstrate that PSK-ε, a novel type of phytosulfokine, positively regulates root elongation and formation of lateral root and root nodule in <i>M. truncatula</i>.