scholarly journals Analysis ofPolygala tenuifoliaTranscriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Hongling Tian ◽  
Xiaoshuang Xu ◽  
Fusheng Zhang ◽  
Yaoqin Wang ◽  
Shuhong Guo ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Illumina Sequencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Local Alignment ◽  
Biosynthetic Pathways ◽  
Molecular Biological Analysis ◽  
Phenylpropanoid Biosynthesis ◽  
Potential Applications ◽  
Pharmaceutical Industries

Radix polygalae, the dried roots ofPolygala tenuifoliaandP. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways ofP. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview ofP. tenuifoliatranscriptome from samples with different years. Using Illumina sequencing, approximately 67.2% of unique sequences were annotated by basic local alignment search tool similarity searches against public sequence databases. We classified the annotated unigenes by using Nr, Nt, GO, COG, and KEGG databases compared with NCBI. We also obtained many candidates CYP450s and UGTs by the analysis of genes in the secondary metabolite biosynthetic pathways, including putative terpenoid backbone and phenylpropanoid biosynthesis pathway. With this transcriptome sequencing, future genetic and genomics studies related to the molecular mechanisms associated with the chemical composition ofP. tenuifoliamay be improved. Genes involved in the enrichment of secondary metabolite biosynthesis-related pathways could enhance the potential applications ofP. tenuifoliain pharmaceutical industries.

scholarly journals The Genetic Regulation of Secondary Metabolic Pathways in Response to Salinity and Drought as Abiotic Stresses

2021 ◽  
Vol 11 (15) ◽  
pp. 6668
Author(s):  
Sameer Hasan Qari ◽  
Ibrahim Tarbiyyah
Keyword(s):  
Complex System ◽  
Secondary Metabolite ◽  
Abiotic Stresses ◽  
Molecular Mechanisms ◽  
Secondary Metabolite Production ◽  
Bioactive Metabolites ◽  
Biosynthetic Pathways ◽  
Plant Genomics ◽  
Metabolite Production ◽  
The Relationship

Global development has generated a plethora of unfavorable and adverse environmental factors for the living organisms in the ecosystem. Plants are sessile organisms, and they are crucial to sustain life on earth. Since plants are sessile, they face a great number of environmental challenges related to abiotic stresses, such as temperature fluctuation, drought, salinity, flood and metal contamination. Salinity and drought are considered major abiotic stresses that negatively affect the plants’ growth and production of useful content. However, plants have evolved various molecular mechanisms to increase their tolerance to these environmental stresses. There is a whole complex system of communication (cross-talk) through massive signaling cascades that are activated and modulated in response to salinity and drought. Secondary metabolites are believed to play significant roles in the plant’s response and resistance to salinity and drought stress. Until recently, attempts to unravel the biosynthetic pathways were limited mainly due to the inadequate plant genomics resources. However, recent advancements in generating high-throughput “omics” datasets, computational tools and functional genomics approach integration have aided in the elucidation of biosynthetic pathways of many plant bioactive metabolites. This review gathers comprehensive knowledge of plants’ complex system that is involved in the response and resistance to salinity and water deficit stresses as abiotic stress. Additionally, it offers clues in determining the genes involved in this complex and measures its activity. It covers basic information regarding the signaling molecules involved in salinity and drought resistance and how plant hormones regulate the cross-talking mechanism with emphasis on transcriptional activity. Moreover, it discusses many studies that illustrate the relationship between salinity and drought and secondary metabolite production. Furthermore, several transcriptome analysis research papers of medicinal plants are illustrated. The aim of this review is to be a key for any researcher that is aspiring to study the relationship between salinity and drought stresses and secondary metabolite production at the transcriptome and transcription level.

scholarly journals De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5681 ◽  
Author(s):  
Li Li ◽  
Mimi Li ◽  
Xiwu Qi ◽  
Xingli Tang ◽  
Yifeng Zhou
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Salt Stress Response ◽  
Glehnia Littoralis ◽  
Plant Signal Transduction

Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.

scholarly journals Comparative Transcriptome Analysis Uncovers Genes and Pathways Relating to Downy Mildew Resistance in Isabgol (Plantago ovata Forsk.)

2020 ◽  
Author(s):  
Manivel Ponnuchamy ◽  
Sandip Patel ◽  
Jincy Mathew ◽  
Jitendra Kumar ◽  
Nagaraja Reddy Rama Reddy
Keyword(s):  
Downy Mildew ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Control Mechanisms ◽  
Plantago Ovata ◽  
Cell Wall Degrading Enzymes ◽  
Transcriptional Responses ◽  
Molecular Pattern ◽  
Phenylpropanoid Biosynthesis ◽  
Effector Triggered Immunity

Abstract BackgroundIsabgol (Plantago ovata Forsk.) downy mildew (DM), caused by obligate oomycete pathogen Peronospora plantaginis Underwood., is the single most damaging disease of Isabgol. However, reports on the genes and pathways involved in mediating resistance are still unknown.ResultsIn the present study, transcriptomic analysis was carried out by next generation sequencing of DM infected and uninfected leaves of resistant and susceptible genotypes to understand the genetic mechanisms underlie the host-plant resistance. A total of 33.47 million reads were generated and de novo assembled and annotated. The assembly using Trinity yielded 38803, 40175, 45451 and 39533 non-redundant transcript contigs, respectively in susceptible infected, Susceptible uninfected, Resistant infected and resistant uninfected samples. More than 90% of coding DNA sequence (CDS) predicted were annotated using BLAST search. Isabgol transcriptome showed the highest similarity to Sesamum indicum (41-59%) followed by Erythranthe guttata (10-13%). Putative CDS encoding Pathogen associated Molecular Pattern (PAMP)-triggered immunity (PTI), Effector-Triggered Immunity (ETI), Cell wall degrading enzymes, Phytohormone signalling and Phenylpropanoid biosynthesis pathways involved in host-pathogen interaction were identified in addition to the identification of several candidate resistance (R) genes enriched in response to DM infection. We identified significantly differentially expressed genes (DEGs) genes; 6928 DEGs in resistant uninfected (RU) vs resistant infected (RI) of DPO-185 (resistant) genotype and 8779 susceptible uninfected (SU) vs susceptible infected (SI) of DPO-14 (susceptible) genotype. Expression of 11 genes involved in plant defense quantified accordingly using RT-qPCR.ConclusionsThis study for the first time provides the glimpse of transcriptional responses to the DM resistance in Isabgol. The genes and pathways will be helpful in further investigating the molecular mechanisms associated with DM disease resistance in Isabgol and to develop control mechanisms accordingly.

scholarly journals Time-series expression profiling of sugarcane leaves infected withPuccinia kuehniireveals an ineffective defense system leading to susceptibility

2019 ◽  
Author(s):  
Fernando Henrique Correr ◽  
Guilherme Kenichi Hosaka ◽  
Sergio Gregorio Perez Gomez ◽  
Mariana Cicarelli Cia ◽  
Claudia Barros Monteiro Vitorello ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Defense Responses ◽  
Recognition System ◽  
Resistance Mechanisms ◽  
Initial Time ◽  
Infected Leaf ◽  
Regulatory Pathways ◽  
Time Points ◽  
Phenylpropanoid Biosynthesis

AbstractPuccinia kuehniiis an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak in Australia. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by the stress induced byP. kuehnii. Here we investigated changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at 0, 12, 24, 48 hours after inoculation (hai), 5 and 12 days after inoculation (dai). Ade novotranscriptome was assembled with preprocessed reads, filtering out potential fungal sequences to focus on plant transcripts. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 hai and 12 dai, coinciding with the events of spore germination, haustoria post-penetration and post-sporulation. During the first 24 hours, a lack of transcripts involved with resistance mechanisms was revealed by underrepresentation of hypersensitive and defense responses. However, two days after inoculation, upregulation of genes involved with immune response regulation provided evidence of some potential defense response. Events related to biotic stress and phenylpropanoid biosynthesis pathways were predominantly downregulated in the initial time points, but expression was later restored to basal levels. Similar waves of expression were apparent for sets of genes in photosynthesis and oxidative processes, whose initial repression could avoid production of signaling molecules. Their subsequent upregulation possibly restored carbohydrate metabolism, ensuring pathogen nutritional requirements were met. Our results support the hypothesis thatP. kuehniiinitially suppressed sugarcane genes involved in plant defense systems. Late overexpression of specific regulatory pathways also suggests the possibility of an inefficient recognition system by a susceptible sugarcane genotype.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ba Van Vu ◽  
Quyet Nguyen ◽  
Yuki Kondo-Takeoka ◽  
Toshiki Murata ◽  
Naoki Kadotani ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number ◽  
Rna Silencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Pyricularia Oryzae ◽  
Transcriptional Gene Silencing ◽  
Physical Interaction ◽  
Uncharacterized Protein ◽  
Form Complex

AbstractTransposable elements are common targets for transcriptional and post-transcriptional gene silencing in eukaryotic genomes. However, the molecular mechanisms responsible for sensing such repeated sequences in the genome remain largely unknown. Here, we show that machinery of homologous recombination (HR) and RNA silencing play cooperative roles in copy number-dependent de novo DNA methylation of the retrotransposon MAGGY in the fungusPyricularia oryzae. Genetic and physical interaction studies revealed thatRecAdomain-containing proteins, includingP. oryzaehomologs ofRad51, Rad55, andRad57, together with an uncharacterized protein, Ddnm1, form complex(es) and mediate either the overall level or the copy number-dependence of de novo MAGGY DNA methylation, likely in conjunction with DNA repair. Interestingly,P. oryzaemutants of specific RNA silencing components (MoDCL1andMoAGO2)were impaired in copy number-dependence of MAGGY methylation. Co-immunoprecipitation of MoAGO2 and HR components suggested a physical interaction between the HR and RNA silencing machinery in the process.

scholarly journals The Prion-Like Spreading of Alpha-Synuclein in Parkinson’s Disease: Update on Models and Hypotheses

2021 ◽  
Vol 22 (15) ◽  
pp. 8338
Author(s):  
Asad Jan ◽  
Nádia Pereira Gonçalves ◽  
Christian Bjerggaard Vaegter ◽  
Poul Henning Jensen ◽  
Nelson Ferreira
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Alpha Synuclein ◽  
Experimental Models ◽  
Cellular Factors ◽  
Recent Developments ◽  
Novel Targets ◽  
Presynaptic Protein

The pathological aggregation of the presynaptic protein α-synuclein (α-syn) and propagation through synaptically coupled neuroanatomical tracts is increasingly thought to underlie the pathophysiological progression of Parkinson’s disease (PD) and related synucleinopathies. Although the precise molecular mechanisms responsible for the spreading of pathological α-syn accumulation in the CNS are not fully understood, growing evidence suggests that de novo α-syn misfolding and/or neuronal internalization of aggregated α-syn facilitates conformational templating of endogenous α-syn monomers in a mechanism reminiscent of prions. A refined understanding of the biochemical and cellular factors mediating the pathological neuron-to-neuron propagation of misfolded α-syn will potentially elucidate the etiology of PD and unravel novel targets for therapeutic intervention. Here, we discuss recent developments on the hypothesis regarding trans-synaptic propagation of α-syn pathology in the context of neuronal vulnerability and highlight the potential utility of novel experimental models of synucleinopathies.

scholarly journals Examination of the Transcriptional Response to LaMIR166a Overexpression in Larix kaempferi (Lamb.) Carr

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 576
Author(s):  
Yanru Fan ◽  
Wanfeng Li ◽  
Zhexin Li ◽  
Shaofei Dang ◽  
Suying Han ◽  
...  
Keyword(s):  
Cell Lines ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Pearson Correlation ◽  
Transcriptional Response ◽  
Correlation Coefficients ◽  
Embryonic Cell ◽  
Larix Kaempferi ◽  
Transgenic Cell

The study of somatic embryogenesis can provide insight into early plant development. We previously obtained LaMIR166a-overexpressing embryonic cell lines of Larix kaempferi (Lamb.) Carr. To further elucidate the molecular mechanisms associated with miR166 in this species, the transcriptional profiles of wild-type (WT) and three LaMIR166a-overexpressing transgenic cell lines were subjected to RNA sequencing using the Illumina NovaSeq 6000 system. In total, 203,256 unigenes were generated using Trinity de novo assembly, and 2467 differentially expressed genes were obtained by comparing transgenic and WT lines. In addition, we analyzed the cleaved degree of LaMIR166a target genes LaHDZ31–34 in different transgenic cell lines by detecting the expression pattern of LaHdZ31–34, and their cleaved degree in transgenic cell lines was higher than that in WT. The downstream genes of LaHDZ31–34 were identified using Pearson correlation coefficients. Yeast one-hybrid and dual-luciferase report assays revealed that the transcription factors LaHDZ31–34 could bind to the promoters of LaPAP, LaPP1, LaZFP5, and LaPHO1. This is the first report of gene expression changes caused by LaMIR166a overexpression in Japanese larch. These findings lay a foundation for future studies on the regulatory mechanism of miR166.

scholarly journals Nanocomposite scaffolds for accelerating chronic wound healing by enhancing angiogenesis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hamed Nosrati ◽  
Reza Aramideh Khouy ◽  
Ali Nosrati ◽  
Mohammad Khodaei ◽  
Mehdi Banitalebi-Dehkordi ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Wound Healing ◽  
Tissue Regeneration ◽  
Molecular Mechanisms ◽  
Healing Process ◽  
The Body ◽  
Key Factors ◽  
Potential Applications ◽  
Nanocomposite Scaffolds

AbstractSkin is the body’s first barrier against external pathogens that maintains the homeostasis of the body. Any serious damage to the skin could have an impact on human health and quality of life. Tissue engineering aims to improve the quality of damaged tissue regeneration. One of the most effective treatments for skin tissue regeneration is to improve angiogenesis during the healing period. Over the last decade, there has been an impressive growth of new potential applications for nanobiomaterials in tissue engineering. Various approaches have been developed to improve the rate and quality of the healing process using angiogenic nanomaterials. In this review, we focused on molecular mechanisms and key factors in angiogenesis, the role of nanobiomaterials in angiogenesis, and scaffold-based tissue engineering approaches for accelerated wound healing based on improved angiogenesis.

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