cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21541393.v1
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>.
DOI: 10.6084/m9.figshare.18517873
title: Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (<i>Triticum aestivum</i> L.)

description: Calmodulin (<i>CaM</i>) and calmodulin-like (<i>CML</i>) genes are widely involved in plant growth and development and mediating plant stress tolerance. However, the whole genome scale studies about <i>CaM</i> and <i>CML</i> gene families have not been done in wheat, and the possible functions of most wheat <i>CaM/CML</i> gene members are still unknown. In this study, a total of 18 <i>TaCaM</i> and 230 <i>TaCML</i> gene members were identified in wheat genome. Among these genes, 28 <i>TaCaM/CML</i> gene members have 74 duplicated copies, while 21 genes have 48 transcript variants, resulting in 321 putative <i>TaCaM/CML</i> transcripts totally. Phylogenetic tree analysis showed that they can be classified into 7 subfamilies. Similar gene structures and protein domains can be found in members of the same gene cluster. The <i>TaCaM/CML</i> genes were spread among all 21 chromosomes with unbalanced distributions, while most of the gene clusters contained 3 homoeologous genes located in the same homoeologous chromosome group. Synteny analysis showed that most of <i>TaCaM/CMLs</i> gene members can be found with 1–4 paralogous genes in <i>T. turgidum</i> and <i>Ae. Tauschii</i>. High numbers of <i>cis</i>-acting elements related to plant hormones and stress responses can be observed in the promoters of <i>TaCaM/CMLs</i>. The spatiotemporal expression patterns showed that most of the <i>TaCaM/TaCML</i> genes can be detected in at least one tissue. The expression levels of <i>TaCML17, 21, 30, 50, 59</i> and <i>75</i> in the root or shoot can be up-regulated by abiotic stresses, suggesting that <i>TaCML17, 21, 30, 50, 59</i> and <i>75</i> may be related with responses to abiotic stresses in wheat. The spatiotemporal expression patterns of <i>TaCaM/CML</i> genes indicated they may be involved widely in wheat growth and development. Our results provide important clues for exploring functions of <i>TaCaMs/CMLs</i> in growth and development as well as responses to abiotic stresses in wheat in the future.
DOI: 10.6084/m9.figshare.18517873.v1
title: Genome-wide identification and expression analysis of calmodulin and calmodulin-like genes in wheat (<i>Triticum aestivum</i> L.)

description: Calmodulin (<i>CaM</i>) and calmodulin-like (<i>CML</i>) genes are widely involved in plant growth and development and mediating plant stress tolerance. However, the whole genome scale studies about <i>CaM</i> and <i>CML</i> gene families have not been done in wheat, and the possible functions of most wheat <i>CaM/CML</i> gene members are still unknown. In this study, a total of 18 <i>TaCaM</i> and 230 <i>TaCML</i> gene members were identified in wheat genome. Among these genes, 28 <i>TaCaM/CML</i> gene members have 74 duplicated copies, while 21 genes have 48 transcript variants, resulting in 321 putative <i>TaCaM/CML</i> transcripts totally. Phylogenetic tree analysis showed that they can be classified into 7 subfamilies. Similar gene structures and protein domains can be found in members of the same gene cluster. The <i>TaCaM/CML</i> genes were spread among all 21 chromosomes with unbalanced distributions, while most of the gene clusters contained 3 homoeologous genes located in the same homoeologous chromosome group. Synteny analysis showed that most of <i>TaCaM/CMLs</i> gene members can be found with 1–4 paralogous genes in <i>T. turgidum</i> and <i>Ae. Tauschii</i>. High numbers of <i>cis</i>-acting elements related to plant hormones and stress responses can be observed in the promoters of <i>TaCaM/CMLs</i>. The spatiotemporal expression patterns showed that most of the <i>TaCaM/TaCML</i> genes can be detected in at least one tissue. The expression levels of <i>TaCML17, 21, 30, 50, 59</i> and <i>75</i> in the root or shoot can be up-regulated by abiotic stresses, suggesting that <i>TaCML17, 21, 30, 50, 59</i> and <i>75</i> may be related with responses to abiotic stresses in wheat. The spatiotemporal expression patterns of <i>TaCaM/CML</i> genes indicated they may be involved widely in wheat growth and development. Our results provide important clues for exploring functions of <i>TaCaMs/CMLs</i> in growth and development as well as responses to abiotic stresses in wheat in the future.
DOI: 10.6084/m9.figshare.20291466
title: Altered carbon status in <i>Glycine max</i> hairy roots induced by <i>Agrobacterium rhizogenes</i>

description: Plants fix CO<sub>2</sub> into carbohydrates through photosynthesis, and various organisms interact with plants to obtain carbohydrates. <i>Agrobacterium rhizogenes</i> is a soil bacterium known as a plant pathogen that induces hairy root disease. Through <i>A. rhizogenes</i>-plant interactions, transfer-DNA (T-DNA) of the Ri plasmid is inserted into the host plant genome, leading to excessive formation of hairy roots and the synthesis of opines that are carbon and nitrogen sources for <i>A. rhizogenes</i>. In this study, we analyzed the carbohydrate contents in soybean (<i>Glycine max</i>) hairy roots. We found that the starch content was strongly increased in hairy roots, whereas the glucose was significantly decreased. On the other hand, no significant differences were observed in sucrose levels between the main roots and hairy roots of <i>A. rhizogenes</i>-inoculated plants. This result suggests that <i>A. rhizogenes</i> infection caused a change in primary carbon metabolism in the host plant cells.
DOI: 10.6084/m9.figshare.20291466.v1
title: Altered carbon status in <i>Glycine max</i> hairy roots induced by <i>Agrobacterium rhizogenes</i>

description: Plants fix CO<sub>2</sub> into carbohydrates through photosynthesis, and various organisms interact with plants to obtain carbohydrates. <i>Agrobacterium rhizogenes</i> is a soil bacterium known as a plant pathogen that induces hairy root disease. Through <i>A. rhizogenes</i>-plant interactions, transfer-DNA (T-DNA) of the Ri plasmid is inserted into the host plant genome, leading to excessive formation of hairy roots and the synthesis of opines that are carbon and nitrogen sources for <i>A. rhizogenes</i>. In this study, we analyzed the carbohydrate contents in soybean (<i>Glycine max</i>) hairy roots. We found that the starch content was strongly increased in hairy roots, whereas the glucose was significantly decreased. On the other hand, no significant differences were observed in sucrose levels between the main roots and hairy roots of <i>A. rhizogenes</i>-inoculated plants. This result suggests that <i>A. rhizogenes</i> infection caused a change in primary carbon metabolism in the host plant cells.
DOI: 10.6084/m9.figshare.21647372
title: Comparative transcriptome analysis of the effects of friction and exogenous gibberellin on germination in <i>Abrus cantoniensis</i>

description: The seeds of <i>Abrus cantoniensis</i> (<i>A. cantonensis</i>) have dormancy characteristics with very low germination under natural conditions. In general, its seed dormancy could be broken by friction or soaking with exogenous gibberellins (GA<sub>3</sub>). To date, the molecular mechanism underlying the effects of GA<sub>3</sub> and friction on its seed germination is unclear. In this study, we tested the effects of different treatments, including soaking in sterile water (G1), friction (G2), soaking in GA<sub>3</sub> (G3), combined treatment of friction, and GA<sub>3</sub> (G4)) on seed germination. Then, we have investigated the seed transcriptome profiles corresponding to the different treatments by RNA sequencing. The results showed that seed germination was significantly increased by combined treatment with friction and GA<sub>3</sub>. RNA-Seq analysis generated 84.80 gigabases (Gb) of sequences. 82,996 out of 121,776 unigenes were annotated. Comparative transcriptome analysis observed that 1,130, 1,097, and 708 unigenes were deferentially expressed in G1 vs. G2, G1 vs. G3, and G1 vs. G4 groups, respectively. Additionally, 20 putatively candidate genes related to seed germination, including <i>CYP78A5, Bg</i>7s, <i>GA-20-ox, rd22, MYB</i>4, <i>LEA, CHS</i>, and <i>STH</i>-2, and other potential candidates with abundant expression were identified. Our findings provide first insights into gene expression profiles and physiological response for friction combined with GA<sub>3</sub> on <i>A. cantoniensis</i> seed germination.
DOI: 10.6084/m9.figshare.21647372.v1
title: Comparative transcriptome analysis of the effects of friction and exogenous gibberellin on germination in <i>Abrus cantoniensis</i>

description: The seeds of <i>Abrus cantoniensis</i> (<i>A. cantonensis</i>) have dormancy characteristics with very low germination under natural conditions. In general, its seed dormancy could be broken by friction or soaking with exogenous gibberellins (GA<sub>3</sub>). To date, the molecular mechanism underlying the effects of GA<sub>3</sub> and friction on its seed germination is unclear. In this study, we tested the effects of different treatments, including soaking in sterile water (G1), friction (G2), soaking in GA<sub>3</sub> (G3), combined treatment of friction, and GA<sub>3</sub> (G4)) on seed germination. Then, we have investigated the seed transcriptome profiles corresponding to the different treatments by RNA sequencing. The results showed that seed germination was significantly increased by combined treatment with friction and GA<sub>3</sub>. RNA-Seq analysis generated 84.80 gigabases (Gb) of sequences. 82,996 out of 121,776 unigenes were annotated. Comparative transcriptome analysis observed that 1,130, 1,097, and 708 unigenes were deferentially expressed in G1 vs. G2, G1 vs. G3, and G1 vs. G4 groups, respectively. Additionally, 20 putatively candidate genes related to seed germination, including <i>CYP78A5, Bg</i>7s, <i>GA-20-ox, rd22, MYB</i>4, <i>LEA, CHS</i>, and <i>STH</i>-2, and other potential candidates with abundant expression were identified. Our findings provide first insights into gene expression profiles and physiological response for friction combined with GA<sub>3</sub> on <i>A. cantoniensis</i> seed germination.
DOI: 10.6084/m9.figshare.17704641
title: A plant cell wall-associated kinase encoding gene is dramatically downregulated during nematode infection of potato

description: Plant cell wall associated kinases (WAKs) and WAK-like kinases (WAKLs) have been increasingly recognized as important regulators of plant immunity against various plant pathogens. However, the role of the <i>WAK</i>/<i>WAKL</i> family in plant-nematode interactions remains to be determined. Here, we analyzed a <i>WAK</i>-encoding gene (<i>Soltu.DM.02G029720.1</i>) from potato (<i>Solanum tuberosum</i>). The <i>Soltu.DM.02G029720.1</i> encoded protein contains domains characteristic of WAK/WAKL proteins and shows the highest similarity to SlWAKL2 from tomato (<i>S. lycopersicum</i>). We thus named the gene as <i>StWAKL2</i>. Phylogenetic analysis of a wide range of plant WAKs/WAKLs further revealed close similarity of StWAKL2 to three WAK/WAKL proteins demonstrated to play a role in disease resistance. To gain insights into the potential regulation and function of <i>StWAKL2</i>, transgenic potato lines containing the <i>StWAKL2</i> promoter fused to the β-glucuronidase (GUS) reporter gene were generated and used to investigate <i>StWAKL2</i> expression during plant development and upon nematode infection. Histochemical analyses revealed that <i>StWAKL2</i> has specific expression patterns in potato leaf and root tissues. During nematode infection, GUS activity was mostly undetected at nematode infection sites over the course of nematode parasitism, although strong GUS activity was observed in root tissues adjacent to the infection region. Furthermore, mining of the transcriptomic data derived from cyst nematode infection of Arabidopsis roots identified a few <i>WAK</i>/<i>WAKL</i> genes, including a <i>StWAKL2</i> homologue, found to be significantly down-regulated in nematode-induced feeding sites. These results indicated that specific suppression of <i>WAK</i>/<i>WAKL</i> genes in nematode-induced feeding sites might be crucial for cyst nematodes to achieve successful infection of host plants. Further studies are needed to uncover the role of <i>WAK</i>/<i>WAKL</i> genes in plant defenses against nematode infection.
DOI: 10.6084/m9.figshare.17704641.v1
title: A plant cell wall-associated kinase encoding gene is dramatically downregulated during nematode infection of potato

description: Plant cell wall associated kinases (WAKs) and WAK-like kinases (WAKLs) have been increasingly recognized as important regulators of plant immunity against various plant pathogens. However, the role of the <i>WAK</i>/<i>WAKL</i> family in plant-nematode interactions remains to be determined. Here, we analyzed a <i>WAK</i>-encoding gene (<i>Soltu.DM.02G029720.1</i>) from potato (<i>Solanum tuberosum</i>). The <i>Soltu.DM.02G029720.1</i> encoded protein contains domains characteristic of WAK/WAKL proteins and shows the highest similarity to SlWAKL2 from tomato (<i>S. lycopersicum</i>). We thus named the gene as <i>StWAKL2</i>. Phylogenetic analysis of a wide range of plant WAKs/WAKLs further revealed close similarity of StWAKL2 to three WAK/WAKL proteins demonstrated to play a role in disease resistance. To gain insights into the potential regulation and function of <i>StWAKL2</i>, transgenic potato lines containing the <i>StWAKL2</i> promoter fused to the β-glucuronidase (GUS) reporter gene were generated and used to investigate <i>StWAKL2</i> expression during plant development and upon nematode infection. Histochemical analyses revealed that <i>StWAKL2</i> has specific expression patterns in potato leaf and root tissues. During nematode infection, GUS activity was mostly undetected at nematode infection sites over the course of nematode parasitism, although strong GUS activity was observed in root tissues adjacent to the infection region. Furthermore, mining of the transcriptomic data derived from cyst nematode infection of Arabidopsis roots identified a few <i>WAK</i>/<i>WAKL</i> genes, including a <i>StWAKL2</i> homologue, found to be significantly down-regulated in nematode-induced feeding sites. These results indicated that specific suppression of <i>WAK</i>/<i>WAKL</i> genes in nematode-induced feeding sites might be crucial for cyst nematodes to achieve successful infection of host plants. Further studies are needed to uncover the role of <i>WAK</i>/<i>WAKL</i> genes in plant defenses against nematode infection.
DOI: 10.6084/m9.figshare.19517985
title: GIGANTEA regulates <i>PAD4</i> transcription to promote pathogen defense against <i>Hyaloperonospora arabidopsidis</i> in <i>Arabidopsis thaliana</i>

description: Plants have evolved a network of complex signaling pathways that allow them to cope with the fluctuations of internal and external environmental cues. GIGANTEA (GI), a well-known, highly conserved plant nuclear protein, has been shown to regulate multiple biological functions in plants such as circadian rhythm, light signaling, cold tolerance, hormone signaling, and photoperiodic flowering. Recently, the role of GI in disease tolerance against different pathogens has come to light; however, a detailed mechanism to understand the role of GI in pathogen defense remains largely unexplained. Here, we report that <i>GIGANTEA</i> is upregulated upon infection with a virulent oomycete pathogen, <i>Hyaloperonospora arabidopsidis</i> (<i>Hpa</i>), in <i>Arabidopsis thaliana</i> accession Col-0. To investigate the role of GI in <i>Arabidopsis</i> defense, we examined the pathogen infection phenotype of <i>gi</i> mutant plants and found that <i>gi-100</i> mutant was highly susceptible to <i>Hpa</i> Noco2 infection. Notably, the quantitative real-time PCR showed that <i>PHYTOALEXIN DEFICIENT4</i> (<i>PAD4</i>) and several PAD4-regulated downstream genes were downregulated upon Noco2 infection in <i>gi-100</i> mutant as compared to Col-0 plants. Furthermore, the chromatin immunoprecipitation results show that GI can directly bind to the intronic region of the <i>PAD4</i> gene, which might explain the mechanism of GI function in regulating disease resistance in plants. Taken together, our results suggest that <i>GI</i> expression is induced upon <i>Hpa</i> pathogen infection and GI can regulate the expression of <i>PAD4</i> to promote resistance against the oomycete pathogen <i>Hyaloperonospora arabidopsidis</i> in <i>Arabidopsis thaliana</i>.
DOI: 10.6084/m9.figshare.20209518
title: Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

description: Brassinosteroids (BRs) regulate of maize (<i>Zea mays</i> L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging, likely by protecting the plant against stem rot and sheath rot. BRs had no significant effect on plant height during late growth, but it increased leaf angle and photosynthetic efficiency, as well as yield and quality traits. Our findings increase our understanding of the regulatory effects of BR on maize root growth and development and the mechanism by which BR improves disease resistance, which could further the potential for using BR to improve maize yield.
DOI: 10.6084/m9.figshare.20209518.v1
title: Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

description: Brassinosteroids (BRs) regulate of maize (<i>Zea mays</i> L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging, likely by protecting the plant against stem rot and sheath rot. BRs had no significant effect on plant height during late growth, but it increased leaf angle and photosynthetic efficiency, as well as yield and quality traits. Our findings increase our understanding of the regulatory effects of BR on maize root growth and development and the mechanism by which BR improves disease resistance, which could further the potential for using BR to improve maize yield.
DOI: 10.6084/m9.figshare.19152849
title: Overexpression of <i>LtKNOX1</i> from <i>Lilium tsingtauense</i> in <i>Nicotiana benthamiana</i> affects the development of leaf morphology

description: Leaves are the main vegetative organs of the aboveground part of plants and play an important role in plant morphogenesis. <i>KNOTTED-LIKE HOMEOBOX</i> (<i>KNOX</i>) plays a crucial role in regulating leaf cell fate and maintaining leaf development. In this study, we analyzed <i>LtKNOX1</i> from <i>Lilium tsingtauense</i> and illustrated its function in transgenic plants. Tissue-specific expression analysis indicated that <i>LtKNOX1</i> was highly expressed in stems, young flower buds, and shoot apical meristems (SAMs). Ectopic overexpression of <i>LtKNOX1</i> in <i>Nicotiana benthamiana</i> suggested that transformants with mild phenotypes were characterized by foliar wrinkles and mildly curled leaves; transformants with intermediate phenotypes showed severely crimped blades and narrow leaf angles, and the most severe phenotypes lacked normal SAMs and leaves. Moreover, the expression levels of genes involved in the regulation of KNOX in transgenic plants were detected, including <i>ASYMMETRIC LEAVES1, PIN-FORMED 1, GA20-oxidase, CUP-SHAPED COTYLEDON 2, CLAVATA 1</i> and <i>WUSCHEL</i>(<i>WUS</i>), and the expression of other genes were down-regulated except <i>WUS</i>. This study contributes to our understanding of the <i>LtKNOX1</i> function.
DOI: 10.6084/m9.figshare.19152849.v1
title: Overexpression of <i>LtKNOX1</i> from <i>Lilium tsingtauense</i> in <i>Nicotiana benthamiana</i> affects the development of leaf morphology

description: Leaves are the main vegetative organs of the aboveground part of plants and play an important role in plant morphogenesis. <i>KNOTTED-LIKE HOMEOBOX</i> (<i>KNOX</i>) plays a crucial role in regulating leaf cell fate and maintaining leaf development. In this study, we analyzed <i>LtKNOX1</i> from <i>Lilium tsingtauense</i> and illustrated its function in transgenic plants. Tissue-specific expression analysis indicated that <i>LtKNOX1</i> was highly expressed in stems, young flower buds, and shoot apical meristems (SAMs). Ectopic overexpression of <i>LtKNOX1</i> in <i>Nicotiana benthamiana</i> suggested that transformants with mild phenotypes were characterized by foliar wrinkles and mildly curled leaves; transformants with intermediate phenotypes showed severely crimped blades and narrow leaf angles, and the most severe phenotypes lacked normal SAMs and leaves. Moreover, the expression levels of genes involved in the regulation of KNOX in transgenic plants were detected, including <i>ASYMMETRIC LEAVES1, PIN-FORMED 1, GA20-oxidase, CUP-SHAPED COTYLEDON 2, CLAVATA 1</i> and <i>WUSCHEL</i>(<i>WUS</i>), and the expression of other genes were down-regulated except <i>WUS</i>. This study contributes to our understanding of the <i>LtKNOX1</i> function.