De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L.

Abstract:

:Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower's yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 pyrosequencing of flower RNA at different developmental stages was performed, generating large databases.In this study, we analyzed 454 sequencing data from different flowering stages in safflower. In total, 1,151,324 raw reads and 1,140,594 clean reads were produced, which were assembled into 51,591 unigenes with an average length of 679 bp and a maximum length of 5109 bp. Among the unigenes, 40,139 were in the early group, 39,768 were obtained from the full group and 28,316 were detected in both samples. With the threshold of "log2 ratio ≥ 1", there were 34,464 differentially expressed genes, of which 18,043 were up-regulated and 16,421 were down-regulated in the early flower library. Based on the annotations of the unigenes, 281 pathways were predicted. We selected 12 putative genes and analyzed their expression levels using quantitative real time-PCR. The results were consistent with the 454 sequencing results. In addition, the expression of chalcone synthase, chalcone isomerase and anthocyanidin synthase, which are involved in safflor yellow biosynthesis and safflower yellow pigment (SYP) content, were analyzed in different flowering periods, indicating that their expression levels were related to SYP synthesis. Moreover, to further confirm the results of the 454 pyrosequencing, full-length cDNA of chalcone isomerase (CHI) and anthocyanidin synthase (ANS) were cloned from safflower petal by RACE (Rapid-amplification of cDNA ends) method according to fragment of the transcriptome.

journal_name

Int J Mol Sci

authors

Liu X,Dong Y,Yao N,Zhang Y,Wang N,Cui X,Li X,Wang Y,Wang F,Yang J,Guan L,Du L,Li H,Li X

doi

10.3390/ijms161025657

subject

Has Abstract

pub_date

2015-10-26 00:00:00

pages

25657-77

issue

10

issn

1422-0067

pii

ijms161025657

journal_volume

16

pub_type

杂志文章
  • Noncanonical reactions of flavoenzymes.

    abstract::Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms131114219

    authors: Sobrado P

    更新日期:2012-11-05 00:00:00

  • Elemental Ingredients in the Macrophage Cocktail: Role of ZIP8 in Host Response to Mycobacterium tuberculosis.

    abstract::Tuberculosis (TB) is a global epidemic caused by the infection of human macrophages with the world's most deadly single bacterial pathogen, Mycobacterium tuberculosis (M.tb). M.tb resides in a phagosomal niche within macrophages, where trace element concentrations impact the immune response, bacterial metal metabolism...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms18112375

    authors: Pyle CJ,Azad AK,Papp AC,Sadee W,Knoell DL,Schlesinger LS

    更新日期:2017-11-09 00:00:00

  • Polymorphic Forms of Valinomycin Investigated by NMR Crystallography.

    abstract::A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously availa...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21144907

    authors: Czernek J,Brus J

    更新日期:2020-07-11 00:00:00

  • Platelet-Rich Plasma Promotes the Proliferation of Human Keratinocytes via a Progression of the Cell Cycle. A Role of Prolidase.

    abstract::Although the role of platelet-rich plasma (PRP) in tissue regeneration has been confirmed in many studies, the mechanism of this process is still not fully understood. Human keratinocytes (HaCaT) cells were used as an experimental model for studies on the effects of PRP on cell proliferation, migration, collagen biosy...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms22020936

    authors: Misiura M,Guszczyn T,Oscilowska I,Baszanowska W,Palka J,Miltyk W

    更新日期:2021-01-19 00:00:00

  • Using Proteomics to Understand How Leishmania Parasites Survive inside the Host and Establish Infection.

    abstract::Leishmania is a protozoan parasite that causes a wide range of different clinical manifestations in mammalian hosts. It is a major public health risk on different continents and represents one of the most important neglected diseases. Due to the high toxicity of the drugs currently used, and in the light of increasing...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms17081270

    authors: Veras PS,Bezerra de Menezes JP

    更新日期:2016-08-19 00:00:00

  • Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis.

    abstract::Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms19092478

    authors: Dong Q,Duan D,Zhao S,Xu B,Luo J,Wang Q,Huang D,Liu C,Li C,Gong X,Mao K,Ma F

    更新日期:2018-08-21 00:00:00

  • Mixed-Generation PAMAM G3-G0 Megamer as a Drug Delivery System for Nimesulide: Antitumor Activity of the Conjugate Against Human Squamous Carcinoma and Glioblastoma Cells.

    abstract::Polyhydroxylated dendrimer was synthesized from poly(amidoamine) (PAMAM) dendrimer generation 3 by addition of glycidol (G3gl). G3gl megamer was further modified by binding PAMAM G0 dendrimers by activation of G3gl with p-nitrophenylchloroformate, followed by the addition of excess PAMAM G0 and purification using dial...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20204998

    authors: Zaręba M,Sareło P,Kopaczyńska M,Białońska A,Uram Ł,Walczak M,Aebisher D,Wołowiec S

    更新日期:2019-10-09 00:00:00

  • Chromatin structure following UV-induced DNA damage-repair or death?

    abstract::In eukaryotes, DNA is compacted into a complex structure known as chromatin. The unravelling of DNA is a crucial step in DNA repair, replication, transcription and recombination as this allows access to DNA for these processes. Failure to package DNA into the nucleosome, the individual unit of chromatin, can lead to g...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms12118063

    authors: Farrell AW,Halliday GM,Lyons JG

    更新日期:2011-01-01 00:00:00

  • Extracellular-Signal Regulated Kinase: A Central Molecule Driving Epithelial-Mesenchymal Transition in Cancer.

    abstract::Epithelial-mesenchymal transition (EMT) is a reversible cellular process, characterized by changes in gene expression and activation of proteins, favoring the trans-differentiation of the epithelial phenotype to a mesenchymal phenotype. This process increases cell migration and invasion of tumor cells, progression of ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20122885

    authors: Olea-Flores M,Zuñiga-Eulogio MD,Mendoza-Catalán MA,Rodríguez-Ruiz HA,Castañeda-Saucedo E,Ortuño-Pineda C,Padilla-Benavides T,Navarro-Tito N

    更新日期:2019-06-13 00:00:00

  • The Genomics and Molecular Biology of Natural Killer/T-Cell Lymphoma: Opportunities for Translation.

    abstract::Extranodal NK/T-cell lymphoma, nasal type (ENKTL), is an aggressive malignancy with a poor prognosis. While the introduction of L-asparaginase in the treatment of this disease has significantly improved the prognosis, the outcome of patients relapsing after asparaginase-based chemotherapy, which occurs in up to 50% of...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19071931

    authors: de Mel S,Soon GS,Mok Y,Chung TH,Jeyasekharan AD,Chng WJ,Ng SB

    更新日期:2018-06-30 00:00:00

  • Bioactive Phytochemicals from Wild Arbutus unedo L. Berries from Different Locations in Portugal: Quantification of Lipophilic Components.

    abstract::The lipophilic composition of wild Arbutus unedo L. berries, collected from six locations in Penacova (center of Portugal), as well as some general chemical parameters, namely total soluble solids, pH, titratable acidity, total phenolic content and antioxidant activity was studied in detail to better understand its po...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms160614194

    authors: Fonseca DF,Salvador ÂC,Santos SA,Vilela C,Freire CS,Silvestre AJ,Rocha SM

    更新日期:2015-06-23 00:00:00

  • Copper-Free 'Click' Chemistry-Based Synthesis and Characterization of Carbonic Anhydrase-IX Anchored Albumin-Paclitaxel Nanoparticles for Targeting Tumor Hypoxia.

    abstract::Triple negative breast cancer (TNBC) is a difficult to treat disease due to the absence of the three unique receptors estrogen, progesterone and herceptin-2 (HER-2). To improve the current therapy and overcome the resistance of TNBC, there is unmet need to develop an effective targeted therapy. In this regard, one of ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms19030838

    authors: Tatiparti K,Sau S,Gawde KA,Iyer AK

    更新日期:2018-03-13 00:00:00

  • First Identification of RNA-Binding Proteins That Regulate Alternative Exons in the Dystrophin Gene.

    abstract::The Duchenne muscular dystrophy (DMD) gene has a complex expression pattern regulated by multiple tissue-specific promoters and by alternative splicing (AS) of the resulting transcripts. Here, we used an RNAi-based approach coupled with DMD-targeted RNA-seq to identify RNA-binding proteins (RBPs) that regulate splicin...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21207803

    authors: Miro J,Bougé AL,Murauer E,Beyne E,Da Cunha D,Claustres M,Koenig M,Tuffery-Giraud S

    更新日期:2020-10-21 00:00:00

  • Laser induced C(60) cage opening studied by semiclassical dynamics simulation.

    abstract::Laser induced opening of the C(60) cage is studied by a semiclassical electron-radiation-ion dynamics technique. The simulation results indicate that the C(60) cage is abruptly opened immediately after laser excitation. The opening of the C(60) cage induces a quick increase in kinetic energy and a sharp decrease in el...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms12010353

    authors: Tang H,Li H,Dou Y

    更新日期:2011-01-13 00:00:00

  • Synergy between Readthrough and Nonsense Mediated Decay Inhibition in a Murine Model of Cystic Fibrosis Nonsense Mutations.

    abstract::Many heritable genetic disorders arise from nonsense mutations, which generate premature termination codons (PTCs) in transcribed mRNA. PTCs ablate protein synthesis by prematurely terminating the translation of mutant mRNA, as well as reducing mutant mRNA quantity through targeted degradation by nonsense-mediated dec...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms22010344

    authors: McHugh DR,Cotton CU,Hodges CA

    更新日期:2020-12-31 00:00:00

  • Goldfish Leptin-AI and Leptin-AII: Function and Central Mechanism in Feeding Control.

    abstract::In mammals, leptin is a peripheral satiety factor that inhibits feeding by regulating a variety of appetite-related hormones in the brain. However, most of the previous studies examining leptin in fish feeding were performed with mammalian leptins, which share very low sequence homologies with fish leptins. To elucida...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms17060783

    authors: Yan AF,Chen T,Chen S,Ren CH,Hu CQ,Cai YM,Liu F,Tang DS

    更新日期:2016-05-30 00:00:00

  • Sirtuins and SIRT6 in Carcinogenesis and in Diet.

    abstract::Sirtuins are a highly conserved family of nicotinamide adenine dinucleotide (NAD)-dependent protein lysine modifying enzymes. They are key regulators for a wide variety of cellular and physiological processes such as cell proliferation, differentiation, DNA damage and stress response, genome stability, cell survival, ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20194945

    authors: de Céu Teixeira M,Sanchez-Lopez E,Espina M,Garcia ML,Durazzo A,Lucarini M,Novellino E,Souto SB,Santini A,Souto EB

    更新日期:2019-10-07 00:00:00

  • The HSP90 Family: Structure, Regulation, Function, and Implications in Health and Disease.

    abstract::The mammalian HSP90 family of proteins is a cluster of highly conserved molecules that are involved in myriad cellular processes. Their distribution in various cellular compartments underlines their essential roles in cellular homeostasis. HSP90 and its co-chaperones orchestrate crucial physiological processes such as...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19092560

    authors: Hoter A,El-Sabban ME,Naim HY

    更新日期:2018-08-29 00:00:00

  • SAHBNET, an accessible surface-based elastic network: an application to membrane protein.

    abstract::Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms140611510

    authors: Dony N,Crowet JM,Joris B,Brasseur R,Lins L

    更新日期:2013-05-30 00:00:00

  • Carbon Nanomaterials and LED Irradiation as Antibacterial Strategies against Gram-Positive Multidrug-Resistant Pathogens.

    abstract:BACKGROUND:Due to current antibiotic resistance worldwide, there is an urgent need to find new alternative antibacterial approaches capable of dealing with multidrug-resistant pathogens. Most recent studies have demonstrated the antibacterial activity and non-cytotoxicity of carbon nanomaterials such as graphene oxide ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20143603

    authors: Elias L,Taengua R,Frígols B,Salesa B,Serrano-Aroca Á

    更新日期:2019-07-23 00:00:00

  • Preparation and Characterization of Whey Protein Isolate-DIM Nanoparticles.

    abstract::3,3'-Diindolylmethane (DIM) is a bioactive compound found in Cruciferous vegetables that possesses health benefits such as antioxidant, anticancer, and anti-inflammatory effects. However, hydrophobicity and photolabile limit its pharmaceutical applications. This study aims to prepare and characterize DIM-encapsulated ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20163917

    authors: Khan A,Wang C,Sun X,Killpartrick A,Guo M

    更新日期:2019-08-12 00:00:00

  • Apoptotic Fragmentation of Tricellulin.

    abstract::Apoptotic extrusion of cells from epithelial cell layers is of central importance for epithelial homeostasis. As a prerequisite cell-cell contacts between apoptotic cells and their neighbors have to be dissociated. Tricellular tight junctions (tTJs) represent specialized structures that seal polarized epithelial cells...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20194882

    authors: Janke S,Mittag S,Reiche J,Huber O

    更新日期:2019-10-01 00:00:00

  • Ambiguous Effects of Autophagy Activation Following Hypoperfusion/Ischemia.

    abstract::Autophagy primarily works to counteract nutrient deprivation that is strongly engaged during starvation and hypoxia, which happens in hypoperfusion. Nonetheless, autophagy is slightly active even in baseline conditions, when it is useful to remove aged proteins and organelles. This is critical when the mitochondria an...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19092756

    authors: Ferrucci M,Biagioni F,Ryskalin L,Limanaqi F,Gambardella S,Frati A,Fornai F

    更新日期:2018-09-13 00:00:00

  • Expression of Hypoxia-Inducible Factor 1α (HIF-1α) and Genes of Related Pathways in Altered Gravity.

    abstract::Immune system deterioration in space represents a major risk, which has to be mitigated for exploration-class missions into the solar system. Altered gravitational forces have been shown to regulate adaptation processes in cells of the immune system, which are important for appropriate risk management, monitoring and ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20020436

    authors: Vogel J,Thiel CS,Tauber S,Stockmann C,Gassmann M,Ullrich O

    更新日期:2019-01-20 00:00:00

  • Synergistic Interaction of Phytohormones in Determining Leaf Angle in Crops.

    abstract::Leaf angle (LA), defined as the angle between the plant stem and leaf adaxial side of the blade, generally shapes the plant architecture into a loosen or dense structure, and thus influences the light interception and competition between neighboring plants in natural settings, ultimately contributing to the crop yield...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21145052

    authors: Li X,Wu P,Lu Y,Guo S,Zhong Z,Shen R,Xie Q

    更新日期:2020-07-17 00:00:00

  • Luminal STIM1 Mutants that Cause Tubular Aggregate Myopathy Promote Autophagic Processes.

    abstract::Stromal interaction molecule 1 (STIM1) is a ubiquitously expressed Ca2+ sensor protein that induces permeation of Orai Ca2+ channels upon endoplasmic reticulum Ca2+-store depletion. A drop in luminal Ca2+ causes partial unfolding of the N-terminal STIM1 domains and thus initial STIM1 activation. We compared the STIM1 ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21124410

    authors: Sallinger M,Tiffner A,Schmidt T,Bonhenry D,Waldherr L,Frischauf I,Lunz V,Derler I,Schober R,Schindl R

    更新日期:2020-06-21 00:00:00

  • Insights into the FMNAT Active Site of FAD Synthase: Aromaticity is Essential for Flavin Binding and Catalysis.

    abstract::The last step in the biosynthesis of flavin adenine dinucleotide (FAD) is considered a target for the design of antimicrobial drugs because it is carried out by two non-homologous proteins in eukaryotic and prokaryotic organisms. Monofunctional FMN: adenylyltransferases (FMNAT) in Eukarya and FMNAT modules of bifuncti...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21103738

    authors: Serrano A,Arilla-Luna S,Medina M

    更新日期:2020-05-25 00:00:00

  • Curcumin Ameliorates Benzo[a]pyrene-Induced DNA Damages in Stomach Tissues of Sprague-Dawley Rats.

    abstract::Benzo[a]pyrene (BaP) is a well-known carcinogen formed during the cooking process. Although BaP exposure has been implicated as one of the risk factors for lung cancer in animals and humans, there are only limited data on BaP-induced gastrointestinal cancer. Therefore, this study investigated the protective effects of...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20225533

    authors: Kim KS,Kim NY,Son JY,Park JH,Lee SH,Kim HR,Kim B,Kim YG,Jeong HG,Lee BM,Kim HS

    更新日期:2019-11-06 00:00:00

  • 3D Bone Morphology Alters Gene Expression, Motility, and Drug Responses in Bone Metastatic Tumor Cells.

    abstract::Patients with advanced skeletal metastases arising from primary cancers including breast, lung, and prostate suffer from extreme pain, bone loss, and frequent fractures. While the importance of interactions between bone and tumors is well-established, our understanding of complex cell-cell and cell-microenvironment in...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21186913

    authors: Dadwal UC,Merkel AR,Page JM,Kwakwa KA,Kessler M,Rhoades JA

    更新日期:2020-09-21 00:00:00

  • An Animal Model for Assessing the Effects of Hydroxyurea Exposure Suggests That the Administration of This Agent to Pregnant Women and Young Infants May Not Be as Safe as We Thought.

    abstract::The cytostatic agent hydroxyurea (HU) has proven to be beneficial for a variety of conditions in the disciplines of oncology, hematology, infectious disease and dermatology. It disrupts the S phase of the cell cycle by inhibiting the ribonucleotide reductase enzyme, thus blocking the transformation of ribonucleotides ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19123986

    authors: Rodríguez-Vázquez L,Martí J

    更新日期:2018-12-11 00:00:00