cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19427003
title: Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony (<i>Paeonia ostii</i>)

description: Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree peony cultivar, ‘Feng Dan’, were sprayed with different concentrations of BR, and the obvious bloom delay was found at the treatment with BR 50 μg/L. The small RNA sequencing and transcriptome sequencing were performed on the petals of tree peony under an untreated control (CK) and the treatment with BR 50 μg/L during four consecutive flowering development stages. A total of 22 known miRNAs belonging to 12 families were identified and 84 novel miRNAs were predicted. Combined with transcriptome data, a total of 376 target genes were predicted for the 18 differentially expressed known miRNAs and 177 target genes were predicted for the 23 differentially expressed novel miRNAs. Additionally, the potential miRNAs and their target genes were identified, including miR156b targeting <i>SPL</i>, miR172a_4 targeting <i>AP2</i> and four novel miRNAs targeting <i>SPA1</i>, and revealed that they might affect the flowering time in tree peony. Collectively, these results would provide a theoretical basis for further analysis of miRNA-guided regulation on flowering period in tree peony.
DOI: 10.6084/m9.figshare.19427003.v1
title: Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony (<i>Paeonia ostii</i>)

description: Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree peony cultivar, ‘Feng Dan’, were sprayed with different concentrations of BR, and the obvious bloom delay was found at the treatment with BR 50 μg/L. The small RNA sequencing and transcriptome sequencing were performed on the petals of tree peony under an untreated control (CK) and the treatment with BR 50 μg/L during four consecutive flowering development stages. A total of 22 known miRNAs belonging to 12 families were identified and 84 novel miRNAs were predicted. Combined with transcriptome data, a total of 376 target genes were predicted for the 18 differentially expressed known miRNAs and 177 target genes were predicted for the 23 differentially expressed novel miRNAs. Additionally, the potential miRNAs and their target genes were identified, including miR156b targeting <i>SPL</i>, miR172a_4 targeting <i>AP2</i> and four novel miRNAs targeting <i>SPA1</i>, and revealed that they might affect the flowering time in tree peony. Collectively, these results would provide a theoretical basis for further analysis of miRNA-guided regulation on flowering period in tree peony.
DOI: 10.6084/m9.figshare.19623720
title: Functional redundancy of <i>OsPIN1</i> paralogous genes in regulating plant growth and development in rice

description: The <i>OsPIN1</i> paralogous genes (<i>OsPIN1a-1d</i>) are important for root and panicle development in rice (<i>Oryza sativa</i> L.). However, the specific role of <i>OsPIN1</i> paralogous genes is still not clear. To understand the specific roles of <i>PIN1</i> paralogs in rice, we generated <i>pin1</i> triple and quadruple mutants by crossing the <i>pin1a pin1b</i> and <i>pin1c pin1d</i> double mutants which we previously created. Compared with the 7-day-old wild type, the <i>pin1a pin1c pin1d</i> and <i>pin1b pin1c pin1d</i> triple mutants showed no obvious phenotype variation except that the <i>pin1a pin1c pin1d</i> triple mutant had shorter primary root and shoot. The <i>pin1a pin1b pin1c</i> and <i>pin1a pin1b pin1d</i> triple mutants exhibited a series of developmental abnormalities, including shorter primary roots, longer root hairs, fewer crown roots and lateral roots, shorter and curved shoots. Furthermore, the <i>pin1a pin1b pin1c pin1d</i> quadruple mutant displayed more severe phenotypic defects which was lethal. In addition, the expression levels of some hormone signal transduction and crown root development related genes, such as <i>OsIAAs, OsARFs, OsRRs</i>, and <i>OsCRLs</i>, were significantly altered in the stem base of all examined <i>pin1</i> multiple mutants. Taken together, our results demonstrated that the four <i>OsPIN1</i> paralogous genes function redundantly in regulating rice growth and development.
DOI: 10.6084/m9.figshare.19623720.v1
title: Functional redundancy of <i>OsPIN1</i> paralogous genes in regulating plant growth and development in rice

description: The <i>OsPIN1</i> paralogous genes (<i>OsPIN1a-1d</i>) are important for root and panicle development in rice (<i>Oryza sativa</i> L.). However, the specific role of <i>OsPIN1</i> paralogous genes is still not clear. To understand the specific roles of <i>PIN1</i> paralogs in rice, we generated <i>pin1</i> triple and quadruple mutants by crossing the <i>pin1a pin1b</i> and <i>pin1c pin1d</i> double mutants which we previously created. Compared with the 7-day-old wild type, the <i>pin1a pin1c pin1d</i> and <i>pin1b pin1c pin1d</i> triple mutants showed no obvious phenotype variation except that the <i>pin1a pin1c pin1d</i> triple mutant had shorter primary root and shoot. The <i>pin1a pin1b pin1c</i> and <i>pin1a pin1b pin1d</i> triple mutants exhibited a series of developmental abnormalities, including shorter primary roots, longer root hairs, fewer crown roots and lateral roots, shorter and curved shoots. Furthermore, the <i>pin1a pin1b pin1c pin1d</i> quadruple mutant displayed more severe phenotypic defects which was lethal. In addition, the expression levels of some hormone signal transduction and crown root development related genes, such as <i>OsIAAs, OsARFs, OsRRs</i>, and <i>OsCRLs</i>, were significantly altered in the stem base of all examined <i>pin1</i> multiple mutants. Taken together, our results demonstrated that the four <i>OsPIN1</i> paralogous genes function redundantly in regulating rice growth and development.
DOI: 10.6084/m9.figshare.17497487
title: Isolation and functional diversification of dihydroflavonol 4-Reductase gene <i>HvDFR</i> from <i>Hosta ventricosa</i> indicate its role in driving anthocyanin accumulation

description: Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. Dihydroflavonol-4reductase (DFR) catalyzes dihydroflavonoids into anthocyanins biosynthesis, which is a key regulatory enzyme of anthocyanin biosynthesis in plants. <i>Hosta ventricosa</i> is an ornamental plant with elegant flowers and rich colorful leaves. How the function of HvDFR contributes to the anthocyanins biosynthesis is still unknown. In this study, the DFR homolog was identified from <i>H. ventricosa</i> and sequence analysis showed that HvDFR possessed the conserved NADPH binding and catalytic domains. A phylogenetic analysis showed that HvDFR was close to the clade formed with MaDFR and HoDFR in Asparagaceae. Gene expression analysis revealed that HvDFR was constitutive expressed in all tissues and expressed highly in flower as well as was positively correlated with anthocyanin content. In addition, the subcellular location of HvDFR showed that is in the nucleus and cell membrane. Overexpression of HvDFR in transgenic tobacco lines enhanced the anthocyanins accumulation along with the key genes upregulated, such as F3H, F3ʹH, ANS, and UFGT. Our results indicated a functional activity of the HvDFR, which provide an insight into the regulation of anthocyanins content in <i>H. ventricosa.</i>
DOI: 10.6084/m9.figshare.17497487.v1
title: Isolation and functional diversification of dihydroflavonol 4-Reductase gene <i>HvDFR</i> from <i>Hosta ventricosa</i> indicate its role in driving anthocyanin accumulation

description: Anthocyanins are natural colorants are synthesized in a branch of the flavonoid pathway. Dihydroflavonol-4reductase (DFR) catalyzes dihydroflavonoids into anthocyanins biosynthesis, which is a key regulatory enzyme of anthocyanin biosynthesis in plants. <i>Hosta ventricosa</i> is an ornamental plant with elegant flowers and rich colorful leaves. How the function of HvDFR contributes to the anthocyanins biosynthesis is still unknown. In this study, the DFR homolog was identified from <i>H. ventricosa</i> and sequence analysis showed that HvDFR possessed the conserved NADPH binding and catalytic domains. A phylogenetic analysis showed that HvDFR was close to the clade formed with MaDFR and HoDFR in Asparagaceae. Gene expression analysis revealed that HvDFR was constitutive expressed in all tissues and expressed highly in flower as well as was positively correlated with anthocyanin content. In addition, the subcellular location of HvDFR showed that is in the nucleus and cell membrane. Overexpression of HvDFR in transgenic tobacco lines enhanced the anthocyanins accumulation along with the key genes upregulated, such as F3H, F3ʹH, ANS, and UFGT. Our results indicated a functional activity of the HvDFR, which provide an insight into the regulation of anthocyanins content in <i>H. ventricosa.</i>
DOI: 10.6084/m9.figshare.24763769
title: Genome-wide expression analysis of <i>LBD</i> genes in tomato (<i>Solanum lycopersicum</i> L.) under different light conditions

description: Lateral organ boundaries (LOB) domain (<i>LBD</i>) genes, a gene family that encodes the transcription factors (TFs) of plants, plays crucial functions in the development and growth of plants. Currently, genome-wide studies of the <i>LBD</i> family are still limited to tomato (<i>Solanum lycopersicum</i> L.), which is considered an important economic crop. In this study, we performed a genome-wide analysis of <i>LBD</i> in tomato. In total, 56 <i>LBDs</i> were found in the tomato genome. Protein alignment and phylogenetic classification showed that <i>LBDs</i> were conserved with other species. Since light emitting diodes (LEDs) light have promising applications for tomato growth. To better understand the potential function of <i>LBDs</i> in response to LED light in tomato, we conducted a genome-wide expression analysis of <i>LBD</i> genes under different light conditions. As expected, different LED lights affected the tomato growth (e.g. hypocotyl length). RNA-seq data showed that eight <i>LBDs</i> in tomato seedlings were differentially expressed under different light treatments, including white, blue, red, and far-red light, compared to the dark-grown condition. It indicates that these <i>LBDs</i> might regulate plant development in different LED light conditions. Interestingly, two <i>LBD</i> genes (<i>SlLBD1</i> and <i>SlLBD2</i>) were found to be differentially expressed in four distinct lights, which might be involved in regulating the plant architecture via a complicated TF network, which can be taken into consideration in further investigation.
DOI: 10.6084/m9.figshare.24763769.v1
title: Genome-wide expression analysis of <i>LBD</i> genes in tomato (<i>Solanum lycopersicum</i> L.) under different light conditions

description: Lateral organ boundaries (LOB) domain (<i>LBD</i>) genes, a gene family that encodes the transcription factors (TFs) of plants, plays crucial functions in the development and growth of plants. Currently, genome-wide studies of the <i>LBD</i> family are still limited to tomato (<i>Solanum lycopersicum</i> L.), which is considered an important economic crop. In this study, we performed a genome-wide analysis of <i>LBD</i> in tomato. In total, 56 <i>LBDs</i> were found in the tomato genome. Protein alignment and phylogenetic classification showed that <i>LBDs</i> were conserved with other species. Since light emitting diodes (LEDs) light have promising applications for tomato growth. To better understand the potential function of <i>LBDs</i> in response to LED light in tomato, we conducted a genome-wide expression analysis of <i>LBD</i> genes under different light conditions. As expected, different LED lights affected the tomato growth (e.g. hypocotyl length). RNA-seq data showed that eight <i>LBDs</i> in tomato seedlings were differentially expressed under different light treatments, including white, blue, red, and far-red light, compared to the dark-grown condition. It indicates that these <i>LBDs</i> might regulate plant development in different LED light conditions. Interestingly, two <i>LBD</i> genes (<i>SlLBD1</i> and <i>SlLBD2</i>) were found to be differentially expressed in four distinct lights, which might be involved in regulating the plant architecture via a complicated TF network, which can be taken into consideration in further investigation.
DOI: 10.6084/m9.figshare.22691610.v1
title: Hypothesis paper: the development of a regulatory layer in P2B autoinhibited Ca<sup>2+</sup>-ATPases may have facilitated plant terrestrialization and animal multicellularization

description: With the appearance of plants and animals, new challenges emerged. These multicellular eukaryotes had to solve for example the difficulties of multifaceted communication between cells and adaptation to new habitats. In this paper, we are looking for one piece of the puzzle that made the development of complex multicellular eukaryotes possible with a focus on regulation of P2B autoinhibited Ca<sup>2+</sup>-ATPases. P2B ATPases pump Ca<sup>2+</sup> out of the cytosol at the expense of ATP hydrolysis, and thereby maintain a steep gradient between the extra- and intracytosolic compartments which is utilized for Ca<sup>2+</sup>-mediated rapid cell signaling. The activity of these enzymes is regulated by a calmodulin (CaM)-responsive autoinhibitory region, which can be located in either termini of the protein, at the C-terminus in animals and at the N-terminus in plants. When the cytoplasmic Ca<sup>2+</sup> level reaches a threshold, the CaM/Ca<sup>2+</sup> complex binds to a calmodulin-binding domain (CaMBD) in the autoinhibitor, which leads to the upregulation of pump activity. In animals, protein activity is also controlled by acidic phospholipids that bind to a cytosolic portion of the pump. Here, we analyze the appearance of CaMBDs and the phospholipid-activating sequence and show that their evolution in animals and plants was independent. Furthermore, we hypothesize that different causes may have initiated the appearance of these regulatory layers: in animals, it is linked to the appearance of multicellularity, while in plants it co-occurs with their water-to-land transition.
DOI: 10.6084/m9.figshare.23018715
title: Methyltransferase-like (METTL) homologues participate in <i>Nicotiana benthamiana</i> antiviral responses

description: Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N<sup>6</sup>-adenosine methylation (m<sup>6</sup>A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m<sup>6</sup>A binding proteins. m<sup>6</sup>A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used <i>Nicotiana benthamiana</i> and plum pox virus (PPV), an RNA virus of the <i>Potyviridae</i> family, to investigated the roles of MTases in plant–virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two <i>N.</i> <i>benthamiana</i> METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and <i>Arabidopsis thaliana</i> FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
DOI: 10.6084/m9.figshare.23018715.v1
title: Methyltransferase-like (METTL) homologues participate in <i>Nicotiana benthamiana</i> antiviral responses

description: Methyltransferase (MTase) enzymes catalyze the addition of a methyl group to a variety of biological substrates. MTase-like (METTL) proteins are Class I MTases whose enzymatic activities contribute to the epigenetic and epitranscriptomic regulation of multiple cellular processes. N<sup>6</sup>-adenosine methylation (m<sup>6</sup>A) is a common chemical modification of eukaryotic and viral RNA whose abundance is jointly regulated by MTases and METTLs, demethylases, and m<sup>6</sup>A binding proteins. m<sup>6</sup>A affects various cellular processes including RNA degradation, post-transcriptional processing, and antiviral immunity. Here, we used <i>Nicotiana benthamiana</i> and plum pox virus (PPV), an RNA virus of the <i>Potyviridae</i> family, to investigated the roles of MTases in plant–virus interaction. RNA sequencing analysis identified MTase transcripts that are differentially expressed during PPV infection; among these, accumulation of a METTL gene was significantly downregulated. Two <i>N.</i> <i>benthamiana</i> METTL transcripts (NbMETTL1 and NbMETTL2) were cloned and further characterized. Sequence and structural analyses of the two encoded proteins identified a conserved S-adenosyl methionine (SAM) binding domain, showing they are SAM-dependent MTases phylogenetically related to human METTL16 and <i>Arabidopsis thaliana</i> FIONA1. Overexpression of NbMETTL1 and NbMETTL2 caused a decrease of PPV accumulation. In sum, our results indicate that METTL homologues participate in plant antiviral responses.
DOI: 10.6084/m9.figshare.22691610
title: Hypothesis paper: the development of a regulatory layer in P2B autoinhibited Ca<sup>2+</sup>-ATPases may have facilitated plant terrestrialization and animal multicellularization

description: With the appearance of plants and animals, new challenges emerged. These multicellular eukaryotes had to solve for example the difficulties of multifaceted communication between cells and adaptation to new habitats. In this paper, we are looking for one piece of the puzzle that made the development of complex multicellular eukaryotes possible with a focus on regulation of P2B autoinhibited Ca<sup>2+</sup>-ATPases. P2B ATPases pump Ca<sup>2+</sup> out of the cytosol at the expense of ATP hydrolysis, and thereby maintain a steep gradient between the extra- and intracytosolic compartments which is utilized for Ca<sup>2+</sup>-mediated rapid cell signaling. The activity of these enzymes is regulated by a calmodulin (CaM)-responsive autoinhibitory region, which can be located in either termini of the protein, at the C-terminus in animals and at the N-terminus in plants. When the cytoplasmic Ca<sup>2+</sup> level reaches a threshold, the CaM/Ca<sup>2+</sup> complex binds to a calmodulin-binding domain (CaMBD) in the autoinhibitor, which leads to the upregulation of pump activity. In animals, protein activity is also controlled by acidic phospholipids that bind to a cytosolic portion of the pump. Here, we analyze the appearance of CaMBDs and the phospholipid-activating sequence and show that their evolution in animals and plants was independent. Furthermore, we hypothesize that different causes may have initiated the appearance of these regulatory layers: in animals, it is linked to the appearance of multicellularity, while in plants it co-occurs with their water-to-land transition.
DOI: 10.6084/m9.figshare.24043243
title: Dynamic changes in the levels of metabolites and endogenous hormones during the germination of <i>Zanthoxylum nitidum</i> (Roxb.) DC. Seeds

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