8 results on '"Fang LIU"'
Search Results
2. A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis.
- Author
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Fang Liu, Peng Zhao, Guangxia Chen, Yongqiang Wang, and Yuanjun Yang
- Subjects
ANTHOCYANINS ,NON-coding RNA ,RNA regulation ,BIOSYNTHESIS ,RNA analysis ,TUBERS ,PLANT-pathogen relationships ,SWEET potatoes - Abstract
Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method
- Author
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Wenbo Li, Fabo Chen, Hong-Fang Liu, and Jian Gao
- Subjects
0106 biological sciences ,0301 basic medicine ,Inbred Strains ,Raphanus ,Gene Expression ,RNA-Seq ,Vegetable Crops ,01 natural sciences ,Plant Roots ,Biochemistry ,Transcriptome ,Anthocyanins ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,Vegetables ,Plant Proteins ,Regulation of gene expression ,Multidisciplinary ,food and beverages ,High-Throughput Nucleotide Sequencing ,Eukaryota ,Agriculture ,Genomics ,Plants ,Experimental Organism Systems ,Biosynthetic process ,Medicine ,Transcriptome Analysis ,Research Article ,Science ,DNA transcription ,Crops ,Brassica ,Biology ,Genes, Plant ,Research and Analysis Methods ,Biosynthesis ,03 medical and health sciences ,DNA-binding proteins ,Genetics ,Gene Regulation ,Gene ,fungi ,Organisms ,Biology and Life Sciences ,Proteins ,Computational Biology ,biology.organism_classification ,Genome Analysis ,Biosynthetic Pathways ,Regulatory Proteins ,030104 developmental biology ,Gene Ontology ,chemistry ,Anthocyanin ,Animal Studies ,Radish ,010606 plant biology & botany ,Transcription Factors ,Crop Science - Abstract
Radish (Raphanus sativus L.), is an important root vegetable crop grown worldwide, and it contains phyto-anthocyanins. However, only limited studies have been conducted to elucidate the molecular mechanisms underlying anthocyanin biosynthesis in the different color variants of the radish fleshy root. In this study, Illumina paired-end RNA-sequencing was employed to characterize the transcriptomic changes in seven different types of radish fleshy roots. Approximately, 126 co-modulated differentially expressed genes were obtained, and most DEGs were more likely to participate in anthocyanin biosynthesis, including two transcription factors RsMYB_9 and RsERF070, and four functional genes RsBRICK1, RsBRI1-like2, RsCOX1, and RsCRK10. In addition, some related genes such as RsCHS, RsCHI, RsANS, RsMT2-4, RsUF3GT, glutathione S-transferase F12, RsUFGT78D2-like and RsUDGT-75C1-like significantly contributed to the regulatory mechanism of anthocyanin biosynthesis in the radish cultivars. Furthermore, gene ontology analysis revealed that the anthocyanin-containing compound biosynthetic process, anthocyanin-containing compound metabolic process, and significantly enriched pathways of the co-modulated DEGs were overrepresented in these cultivars. These results will expand our understanding of the complex molecular mechanism underlying anthocyanin synthesis-related genes in radish.
- Published
- 2019
4. Exposure to endophytic fungi quantitatively and compositionally alters anthocyanins in grape cells
- Author
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Yin-Min Ma, Jin-Zhuo Qu, Man Yu, Ming-Zhi Yang, Xiao-Xia Pan, Han-Bo Zhang, Si-Yu Xiang, Jing-Chao Chen, Ming Zhou, and Fang Liu
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Organoleptic ,Wine ,Plant Science ,Fungus ,01 natural sciences ,Plant use of endophytic fungi in defense ,Anthocyanins ,03 medical and health sciences ,chemistry.chemical_compound ,Dual culture ,Genetics ,Vitis ,Food science ,Anthocyanidin ,biology ,fungi ,Fungi ,food and beverages ,Anthocyanin synthesis ,biology.organism_classification ,Anthocyanidins ,030104 developmental biology ,chemistry ,Anthocyanin ,Fruit ,010606 plant biology & botany - Abstract
Anthocyanins contribute greatly to the organoleptic and biochemical properties of grapes and wines. Although there are broadly documented factors involved in grape anthocyanin synthesis, the present work focused on fungal endophytes and their possible role in grape coloration. Our results showed that exposure to endophytic fungi within a dual culture system differentially affected total anthocyanin concentrations and PAL activities in grape cells. Grape cells dual cultured with fungal strains XH-2, R2-21 and B2-17 showed significant differences of their anthocyanin concentrations were subjected to further analysis of their anthocyanidin compositions. Compared to the no-fungus controls, grape cells exposed to fungal strains XH-2 and R2-21 exhibited quantitative promotion of their total anthocyanidin concentrations by 74% and 28%, respectively, whereas treatment with the fungus B2-17 reduced the anthocyanidin content by 19%. A total of 14 species of anthocyanidins were detected from the grape cells in these experiments. Most interestingly, exposure to any of these fungal strains differentially modified the compositional patterns of grape cellular anthocyanidins. The obvious upregulation of the transcription of VvMYB in grape cells treated with fungal strains XH-2 and R2-21 implies that the increased anthocyanin levels in these grape cells may be due to the activated transcriptional factors. In addition, the exposure of grape cells to extracts of these fungi initiated similar responses of anthocyanin contents and PAL activities to exposure to the living fungi and appeared obvious dosage effects. The influence of fungal endophytes on the coloration of grape berries was also examined in this study.
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- 2019
5. Malvidin 3-Glucoside Modulated Gut Microbial Dysbiosis and Global Metabolome Disrupted in a Murine Colitis Model Induced by Dextran Sulfate Sodium
- Author
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Vivian C.H. Wu, Thomas T.Y. Wang, Robert W. Li, Qingjuan Tang, Fang Liu, and Changhu Xue
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0301 basic medicine ,Male ,Firmicutes ,Colon ,Microbiology ,Anthocyanins ,03 medical and health sciences ,chemistry.chemical_compound ,Metabolomics ,Glucosides ,Ruminococcus gnavus ,RNA, Ribosomal, 16S ,Metabolome ,medicine ,Animals ,Microbiome ,Colitis ,030109 nutrition & dietetics ,biology ,Chemistry ,Dextran Sulfate ,biology.organism_classification ,medicine.disease ,Sphingolipid ,Malvidin ,Gastrointestinal Microbiome ,Mice, Inbred C57BL ,030104 developmental biology ,Dietary Supplements ,Dysbiosis ,Food Science ,Biotechnology - Abstract
Scope This study aims to elucidate the mechanisms of the anthocyanin malvidin 3-glucoside (MV) in alleviating gut dysbiosis using a murine colitis model induced by dextran sulfate sodium (DSS). Methods and results The effect of MV on the structure and function of the colon microbiome and microbial metabolism is evaluated using 16S rRNA gene sequencing, global metabolomics, and a network algorithm based on the random-matrix theory. MV ingestion improved histopathological scores and increased IL10 expression in the colon mucosa of colitis mice. While DSS has a profound effect on the gut microbiome and significantly decreases both microbial richness and evenness, MV further reduces evenness but promotes microbial interactions and restores the Firmicutes/Bacteroidetes ratio repressed by DSS. Moreover, MV reduces the abundance of pathogenic bacteria, such as Ruminococcus gnavus, in colitis mice and has a strong modulatory effect on microbial co-occurrence patterns and gut metabolites. In addition, MV reverses several key inflammatory mediators, including sphingolipid metabolites, from elevated levels in DSS colitis mice. As a bioactive ingredient, MV exerts its effect on the gut microbiome in a mechanism that differs from the whole blueberry. Conclusion MV ingestion ameliorates intestinal inflammation by modulating colon epithelium integrity, gut microbiome, and key inflammatory mediators.
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- 2019
6. RrMYB5- and RrMYB10-regulated flavonoid biosynthesis plays a pivotal role in feedback loop responding to wounding and oxidation in Rosa rugosa
- Author
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Qi Pan, Nachaisin Anupol, Caiyun Wang, Jian Zhao, Changquan Wang, Fang Liu, Yuxiao Shen, Tingting Sun, Jiewei Shi, Hai Chen, Manzhu Bao, Shuhua Yang, Ning Guogui, Duanmu Deqiang, and Jihong Liu
- Subjects
0106 biological sciences ,0301 basic medicine ,oxidation ,Flavonoid ,Plant Science ,Oxidative phosphorylation ,Biology ,Rosa ,01 natural sciences ,Transcriptome ,Anthocyanins ,03 medical and health sciences ,Gene Expression Regulation, Plant ,MYB ,flavonoid ,Gene ,Research Articles ,Plant Proteins ,MYB transcription factor ,chemistry.chemical_classification ,Flavonoids ,Structural gene ,fungi ,food and beverages ,Oxidation response ,Plants, Genetically Modified ,wounding ,Cell biology ,Oxidative Stress ,030104 developmental biology ,Flavonoid biosynthesis ,chemistry ,Rosa rugosa ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology ,Transcription Factors ,Research Article - Abstract
Summary Flavonoids play critical roles in plant responses to various stresses. Few studies have been reported on what the mechanism of activating flavonoid biosynthesis in plant responses to wounding and oxidation is. In this study, flavonoid metabolites and many MYB transcript factors from Rosa rugosa were verified to be induced by wounding and oxidation. RrMYB5 and RrMYB10, which belong to PA1‐ and TT2‐type MYB TFs, respectively, showed extremely high induction. Overexpression of RrMYB5 and RrMYB10 resulted in an increased accumulation of proanthocyanidins in R. rugosa and tobacco by promoting the expression of flavonoid structural genes. Transcriptomic analysis of the transgenic plants showed that most genes, involved in wounding and oxidation response and ABA signalling modulation, were up‐regulated by the overexpression of RrMYB10, which was very much similar to that observed in RrANR and RrDFR overexpression transgenics. RrMYB5 and RrMYB10 physically interacted and mutually activated each other's expressions. They solely or synergistically activated the different sets of flavonoid pathway genes in a bHLH TF EGL3‐independent manner. Eventually, the accumulation of proanthocyanidins enhanced plant tolerance to wounding and oxidative stresses. Therefore, RrMYB5 and RrMYB10 regulated flavonoid synthesis in feedback loop responding to wounding and oxidation in R. rugosa. Our study provides new insights into the regulatory mechanisms of flavonoid biosynthesis by MYB TFs and their essential physiological functions in plant responses to wounding and oxidative stresses.
- Published
- 2018
7. A comparative transcriptome analysis of a wild purple potato and its red mutant provides insight into the mechanism of anthocyanin transformation
- Author
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Changle Ma, Fang Liu, Yuping Bi, Yuanjun Yang, and Jianwei Gao
- Subjects
0106 biological sciences ,0301 basic medicine ,Mutant ,Gene Expression ,lcsh:Medicine ,Plant Science ,01 natural sciences ,Biochemistry ,Transcriptome ,Anthocyanins ,Cytochrome P-450 Enzyme System ,Glucosides ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Vegetables ,MYB ,lcsh:Science ,Plant Proteins ,Multidisciplinary ,Phenylpropanoid ,Pigmentation ,Plant Anatomy ,Transcriptional Control ,Structural gene ,High-Throughput Nucleotide Sequencing ,Eukaryota ,food and beverages ,Genomics ,Plants ,Plant Tubers ,RNA, Plant ,Potato ,Transcriptome Analysis ,Research Article ,Phenylalanine ammonia-lyase ,Biology ,Genes, Plant ,Solanum ,Biosynthesis ,03 medical and health sciences ,Coenzyme A Ligases ,DNA-binding proteins ,Genetics ,Gene Regulation ,Phenylalanine Ammonia-Lyase ,Solanum tuberosum ,Biology and life sciences ,Tubers ,Gene Expression Profiling ,fungi ,lcsh:R ,Wild type ,Organisms ,Proteins ,Computational Biology ,Genome Analysis ,Biosynthetic Pathways ,Regulatory Proteins ,Transformation (genetics) ,030104 developmental biology ,Mutation ,lcsh:Q ,010606 plant biology & botany ,Transcription Factors - Abstract
In this study, a red mutant was obtained through in vitro regeneration of a wild purple potato. High-performance liquid chromatography and Mass spectrometry analysis revealed that pelargonidin-3-O-glucoside and petunidin-3-O-glucoside were main anthocyanins in the mutant and wild type tubers, respectively. In order to thoroughly understand the mechanism of anthocyanin transformation in two materials, a comparative transcriptome analysis of the mutant and wild type was carried out through high-throughput RNA sequencing, and 295 differentially expressed genes (DEGs) were obtained. Real-time qRT-PCR validation of DEGs was consistent with the transcriptome date. The DEGs mainly influenced biological and metabolic pathways, including phenylpropanoid biosynthesis and translation, and biosynthesis of flavone and flavonol. In anthocyanin biosynthetic pathway, the analysis of structural genes expressions showed that three genes, one encoding phenylalanine ammonia-lyase, one encoding 4-coumarate-CoA ligase and one encoding flavonoid 3′,5′-hydroxylasem were significantly down-regulated in the mutant; one gene encoding phenylalanine ammonia-lyase was significantly up-regulated. Moreover, the transcription factors, such as bZIP family, MYB family, LOB family, MADS family, zf-HD family and C2H2 family, were significantly regulated in anthocyanin transformation. Response proteins of hormone, such as gibberellin, abscisic acid and brassinosteroid, were also significantly regulated in anthocyanin transformation. The information contributes to discovering the candidate genes in anthocyanin transformation, which can serve as a comprehensive resource for molecular mechanism research of anthocyanin transformation in potatoes.
- Published
- 2018
8. De novo transcriptome sequencing of radish (Raphanus sativus L.) fleshy roots: analysis of major genes involved in the anthocyanin synthesis pathway.
- Author
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Jian Gao, Wen-Bo Li, Hong-Fang Liu, and Fa-Bo Chen
- Subjects
ANTHOCYANINS ,RADISHES ,METABOLITES ,POLYMERASE chain reaction - Abstract
Background: The HongXin radish (Raphanus sativus L.), which contains the natural red pigment (red radish pigment), is grown in the Fuling district of Chongqing City. However, the molecular mechanisms underlying anthocyanin synthesis for the formation of natural red pigment in the fleshy roots of HongXin radish are not well studied. Results: De novo transcriptome of HX-1 radish, as well as that of the advanced inbred lines HX-2 and HX-3 were characterized using next generation sequencing (NGS) technology. In total, approximately 66.22 million paired-end reads comprising 34, 927 unigenes (N50 = 1, 621 bp) were obtained. Based on sequence similarity search with known proteins, total of 30, 127 (about 86.26%) unigenes were identified. Additionally, functional annotation and classification of these unigenes indicated that most of the unigenes were predominantly enriched in the metabolic process-related terms, especially for the biosynthetic pathways of secondary metabolites. Moreover, majority of the anthocyanin biosynthesis-related genes (ABRGs) involved in the regulation of anthocyanin biosynthesis were identified by targeted search for their annotation. Subsequently, the expression of 15 putative ABRGs involved in the anthocyanin synthesis-related pathways were validated using quantitative real-time polymerase chain reaction (qRT-PCR). Of those, RsPAL2, RsCHS-B2, RsDFR1, RsDFR2, RsFLS, RsMT3 and RsUFGT73B2-like were identified significantly associated with anthocyanin biosynthesis. Especially for RsDFR1, RsDFR2 and RsFLS, of those, RsDFR1 and RsDFR2 were highest enriched in the HX-3 and WG-3, but RsFLS were down-regulated in HX-3 and WG-3. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be act as key regulators in anthocyanin biosynthesis pathway. Conclusions: The assembled radish transcript sequences were analysed to identify the key ABRGs involved in the regulation of anthocyanin biosynthesis. Additionally, the expression patterns of candidate ABRGs involved in the anthocyanin biosynthetic pathway were validated by qRT-PCR. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be acted as key regulators in anthocyanin biosynthesis pathway. This study will enhance our understanding of the biosynthesis and metabolism of anthocyanin in radish. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
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