A Comparative Transcriptome Analysis of Purple and Yellow Fleshed Potato Tubers Reveals Long Non-coding RNAs and their Targets Functioned in Anthocyanin Biosynthesis

Abstract Background: Purple fleshed potato tubers accumulate large amounts of anthocyanin content, servicing as functional foods and high-value feedstock. Long non-coding RNAs (lncRNAs) have been reported to play an important role in anthocyanin synthesis by regulating gene expression in various action modes. However, the mechanism underlying anthocyanin accumulation mediated by lncRNAs in underground organs remains unclear.Results: To excavate the differentially expressed lncRNAs (DE lncRNAs) between purple and yellow fleshed potato tubers, the transcriptome sequencing was performed and a total of 1421 DE lncRNAs were identified. Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that the target genes of these DE lncRNAs were involved in diverse biological processes and pathways for anthocyanin biosynthesis, reflecting the functional diversity of the corresponding lncRNAs. A lncRNA-mRNA interaction network was created based on their correlation to investigate the regulatory relationship among them. Notably, lncRNAs like XLOC_060098 and XLOC_017372 might contribute to anthocyanin synthesis by targeting the key enzyme genes and transcription factor genes in the pathway. Conclusions: The construction of expression profiling of DE lncRNAs and lncRNA-mRNA relationship network is helpful for further unraveling the molecular mechanisms of lncRNAs in anthocyanin synthesis in potato tubers, and provides theory basis for the cultivation of functional potato varieties and the improvement of nutritional quality of other underground crops.

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The Light-Induced WD40-Repeat Transcription Factor DcTTG1 Regulates Anthocyanin Biosynthesis in Dendrobium candidum

Frontiers in Plant Science ◽

10.3389/fpls.2021.633333 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ning Jia ◽

Jingjing Wang ◽

Yajuan Wang ◽

Wei Ye ◽

Jiameng Liu ◽

...

Keyword(s):

Transcription Factor ◽

Molecular Mechanisms ◽

Anthocyanin Biosynthesis ◽

Raw Material ◽

Anthocyanin Synthesis ◽

Anthocyanin Content ◽

Anthocyanin Accumulation ◽

Wd40 Repeat ◽

Strong Light ◽

Dendrobium Candidum

Dendrobium candidum is used as a traditional Chinese medicine and as a raw material in functional foods. D. candidum stems are green or red, and red stems are richer in anthocyanins. Light is an important environmental factor that induces anthocyanin accumulation in D. candidum. However, the underlying molecular mechanisms have not been fully unraveled. In this study, we exposed D. candidum seedlings to two different light intensities and found that strong light increased the anthocyanin content and the expression of genes involved in anthocyanin biosynthesis. Through transcriptome profiling and expression analysis, we identified a WD40-repeat transcription factor, DcTTG1, whose expression is induced by light. Yeast one-hybrid assays showed that DcTTG1 binds to the promoters of DcCHS2, DcCHI, DcF3H, and DcF3′H, and a transient GUS activity assay indicated that DcTTG1 can induce their expression. In addition, DcTTG1 complemented the anthocyanin deficiency phenotype of the Arabidopsis thaliana ttg1-13 mutant. Collectively, our results suggest that light promotes anthocyanin accumulation in D. candidum seedlings via the upregulation of DcTTG1, which induces anthocyanin synthesis-related gene expression.

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Study on cyanidin metabolism in petals of pink-flowered strawberry based on transcriptome sequencing and metabolite analysis

BMC Plant Biology ◽

10.1186/s12870-019-2048-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Li Xue ◽

Jian Wang ◽

Jun Zhao ◽

Yang Zheng ◽

Hai-Feng Wang ◽

...

Keyword(s):

Regulatory Networks ◽

Molecular Mechanisms ◽

Target Genes ◽

Anthocyanin Biosynthesis ◽

Expression Profiles ◽

Expression Patterns ◽

Anthocyanin Synthesis ◽

Integrated Analysis ◽

Intergeneric Hybridization ◽

Significant Differential Expression

Abstract Background Pink-flowered strawberry is a promising new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, a prolonged flowering period and edible fruits. Its flower color ranges from light pink to red. Pigment compounds accumulated in its fruits were the same as in cultivated strawberry fruits, but different from that in its flowers. However, the transcriptional events underlying the anthocyanin biosynthetic pathway have not been fully characterized in petal coloration. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify the key genes, we performed an integrated analysis of the transcriptome and metabolome in petals of pink-flowered strawberry. Results The main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compound. There were no anthocyanins detected in the white-flowered hybrids. A total of 50,285 non-redundant unigenes were obtained from the transcriptome databases involved in red petals of pink-flowered strawberry cultivar Sijihong at three development stages. Amongst the unigenes found to show significant differential expression, 57 were associated with anthocyanin or other flavonoid biosynthesis, in which they were regulated by 241 differentially expressed members of transcription factor families, such as 40 MYBs, 47 bHLHs, and 41 NACs. Based on a comprehensive analysis relating pigment compounds to gene expression profiles, the mechanism of flower coloration was examined in pink-flowered strawberry. A new hypothesis was proposed to explain the lack of color phenotype of the white-flowered strawberry hybrids based on the transcriptome analysis. The expression patterns of FpDFR and FpANS genes corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the major factors that led to the absence of anthocyanins in the white petals of pink-flowered strawberry hybrids. Meanwhile, the competitive effect of FpFLS and FpDFR genes might further inhibit anthocyanin synthesis. Conclusions The data presented herein are important for understanding the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating novel potential target genes to breed valuable pink-flowered strawberry cultivars.

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Elucidating the Mechanisms of Hugan Buzure Granule in the Treatment of Liver Fibrosis via Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/8385706 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Yi Zhu ◽

Ming Qiao ◽

Jianhua Yang ◽

Junping Hu

Keyword(s):

Liver Fibrosis ◽

Rna Polymerase Ii ◽

Molecular Mechanisms ◽

Target Genes ◽

Docking Simulation ◽

Interaction Network ◽

Network Pharmacology ◽

Transcription Activator ◽

Active Ingredients ◽

Oxidoreductase Activity

Objective. To holistically explore the latent active ingredients, targets, and related mechanisms of Hugan buzure granule (HBG) in the treatment of liver fibrosis (LF) via network pharmacology. Methods. First, we collected the ingredients of HBG by referring the TCMSP server and literature and filtered the active ingredients though the criteria of oral bioavailability ≥30% and drug-likeness index ≥0.18. Second, herb-associated targets were predicted and screened based on the BATMAN-TCM and SwissTargetPrediction platforms. Candidate targets related to LF were collected from the GeneCards and OMIM databases. Furthermore, the overlapping target genes were used to construct the protein-protein interaction network and “drug-compound-target-disease” network. Third, GO and KEGG pathway analyses were carried out to illustrate the latent mechanisms of HBG in the treatment of LF. Finally, the combining activities of hub targets with active ingredients were further verified based on software AutoDock Vina. Results. A total of 25 active ingredients and 115 overlapping target genes of HBG and LF were collected. Besides, GO enrichment analysis exhibited that the overlapping target genes were involved in DNA-binding transcription activator activity, RNA polymerase II-specific, and oxidoreductase activity. Simultaneously, the key molecular mechanisms of HBG against LF were mainly involved in PI3K-AKT, MAPK, HIF-1, and NF-κB signaling pathways. Also, molecular docking simulation demonstrated that the key targets of HBG for antiliver fibrosis were IL6, CASP3, EGFR, VEGF, and MAPK. Conclusion. This work validated and predicted the underlying mechanisms of multicomponent and multitarget about HBG in treating LF and provided a scientific foundation for further research.

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PbCOP1.1 Contributes to the Negative Regulation of Anthocyanin Biosynthesis in Pear

Plants ◽

10.3390/plants8020039 ◽

2019 ◽

Vol 8 (2) ◽

pp. 39 ◽

Cited By ~ 4

Author(s):

Meng Wu ◽

Min Si ◽

Xieyu Li ◽

Linyan Song ◽

Jianlong Liu ◽

...

Keyword(s):

Protein Sequence ◽

Molecular Mechanisms ◽

Anthocyanin Biosynthesis ◽

Pcr Analysis ◽

Anthocyanin Synthesis ◽

Light Signaling ◽

Pear Fruit ◽

Phylogenetic Tree Analysis ◽

Expression Levels ◽

Protein Sequence Alignment

The synthesis of anthocyanin in pear (Pyrus bretschneideri) fruit is regulated by light. However, little is known about the molecular mechanisms of pear fruit coloring mediated by upstream light-signaling regulators. Here, the photoresponse factors CONSTITUTIVE PHOTOMORPHOGENIC (COP) 1.1 and 1.2 were cloned from ‘Red Zaosu’ peel to study their functions in pear fruit coloring. The overexpression vectors pBI121-PbCOP1.1 and pBI121-PbCOP1.2 were constructed to analyze their effects on anthocyanin synthesis in pear fruit. A protein sequence alignment and phylogenetic tree analysis revealed that PbCOP1 proteins are highly homologous with those of other species. An analysis of tissue differential expression showed that the greatest expression levels of PbCOP1s occurred in the leaves. Their expression levels increased in the leaves during development, when the leaves changed from red to green. The overexpression of PbCOP1s in the peel resulted in reduced anthocyanin synthesis at the injection sites. A quantitative PCR analysis of the injection sites showed that PbCOP1.1 significantly inhibited the expression of the anthocyanin synthesis-related genes CHI, DFR, UFGT2, bHLH3, HY5 and GST. Based on the above results, we hypothesize that PbCOP1.1 is an anthocyanin synthetic inhibitory factor of pear coloration.

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Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms20184335 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4335 ◽

Cited By ~ 4

Author(s):

Ju Gao ◽

Gaoxing Dai ◽

Weiyong Zhou ◽

Haifu Liang ◽

Juan Huang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Anthocyanin Biosynthesis ◽

Bulked Segregant Analysis ◽

Recessive Gene ◽

Leaf Traits ◽

Anthocyanin Synthesis ◽

Genetic Characteristics ◽

Specific Organ ◽

Flower Organs ◽

Purple Leaf

The anthocyanin biosynthesis of rice is a major concern due to the potential nutritional value. Purple appears in various organs and tissues of rice such as pericarp, flower organs, leaves, leaf sheaths, internodes, ligules, apex, and stigma. At present, there are many studies on the color of rice pericarp, but the gene and mechanism of other organs such as leaves are still unclear, and the gene regulatory network of specific organ coloring has not been systematically understood. In this study, genetic analysis demonstrated that the purple leaf traits of rice were regulated by a recessive gene. The green leaf cultivar Y58S and purple leaf cultivar XianHongB were used to construct the mapping population. A set of near isogenicline (NIL) (BC3F1) was bred via crossing and back-crossing. The generations of BC3F2 appeared to separate four phenotypes, pl1, pl2, pl3, and pl4, due to the occurrence of a purple color in different organs. We constructed three bulked segregant analysis (BSA) pools (pl1–pl2, pl1–pl3, and pl1–pl4) by using the separated generations of BC3F5 and mapped the purple leaf gene plr4 to the vicinity of 27.9–31.1 Mb on chromosome 4. Subsequently, transcriptome sequencing (RNA-Seq) for pl3 and pl2 was used to analyze the differentially expressed genes in the localization interval, where 12 unigenes exhibited differential expression in which two genes (Os04g0577800, Os04g0616400) were downregulated. The two downregulated genes (Os04g0577800 and Os04g0616400) are possible candidate genes because of the recessive genetic characteristics of the purple leaf genes. These results will facilitate the cloning of plr4 and illustrate the molecular mechanisms of the anthocyanin synthesis pathway.

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A Network Pharmacology-Based Study on the Anti-Lung Cancer Effect of Dipsaci Radix

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/7424061 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Jiayan Wu ◽

Shengkun Hong ◽

Xiankuan Xie ◽

Wangmi Liu

Keyword(s):

Lung Cancer ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Molecular Mechanisms ◽

Target Genes ◽

Interaction Network ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Hub Genes ◽

Active Compounds

Objective. Dipsaci Radix (DR) has been used to treat fracture and osteoporosis. Recent reports have shown that myeloid cells from bone marrow can promote the proliferation of lung cancer. However, the action and mechanism of DR has not been well defined in lung cancer. The aim of the present study was to define molecular mechanisms of DR as a potential therapeutic approach to treat lung cancer. Methods. Active compounds of DR with oral bioavailability ≥30% and drug-likeness index ≥0.18 were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform. The potential target genes of the active compounds and bone were identified by PharmMapper and GeneCards, respectively. The compound-target network and protein-protein interaction network were built by Cytoscape software and Search Tool for the Retrieval of Interacting Genes webserver, respectively. GO analysis and pathway enrichment analysis were performed using R software. Results. Our study demonstrated that DR had 6 active compounds, including gentisin, sitosterol, Sylvestroside III, 3,5-Di-O-caffeoylquinic acid, cauloside A, and japonine. There were 254 target genes related to these active compounds as well as to bone. SRC, AKT1, and GRB2 were the top 3 hub genes. Metabolisms and signaling pathways associated with these hub genes were significantly enriched. Conclusions. This study indicated that DR could exhibit the anti-lung cancer effect by affecting multiple targets and multiple pathways. It reflects the traditional Chinese medicine characterized by multicomponents and multitargets. DR could be considered as a candidate for clinical anticancer therapy by regulating bone physiological functions.

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Improving the Anthocyanin Accumulation of Hypocotyls in Radish Sprouts by Hemin-induced NO

10.21203/rs.3.rs-117868/v1 ◽

2020 ◽

Author(s):

Nana Su ◽

Ze Liu ◽

Hui Chen ◽

Mengyang Niu ◽

Jin Cui

Keyword(s):

Nitric Oxide ◽

Transcription Factors ◽

Anthocyanin Biosynthesis ◽

Reductase Activity ◽

Specific Inhibitor ◽

Anthocyanin Synthesis ◽

Zinc Protoporphyrin ◽

Anthocyanin Content ◽

Anthocyanin Accumulation ◽

Radish Sprouts

Abstract Background: The biosynthesis of anthocyanin in the hypocotyls of radish (Raphanus sativus L.) sprouts was enhanced by hemin in our preliminary experiments, but the underlying mechanism is unclear. Here, we found that NO (nitric oxide) exerted an essential role in Hemin-regulated anthocyanin biosynthesis, which was supported by the following results.Results: Hemin boosted anthocyanin as well as NO content. NO-scavenger cPTIO (carboxy-PTIO) significantly attenuated hemin-induced increase of anthocyanin content, transcripts of anthocyanin synthesis related genes and positive transcription factors, implying that NO played a prominent role during hemin-induced anthocyanin biosynthesis. Hemin specific inhibitor ZnPP (Zinc Protoporphyrin) strongly reduced anthocyanin content, while, NO donor SNP (Sodium Nitroprusside) addition considerably reversed this inhibition and by contrast, resulted in a significant increase in anthocyanin accumulation, closely paralleling the transcripts of structural genes and transcription factors. Moreover, NO content, NR (nitrate reductase) activity and expression level of NOA (nitric oxide associated factor) were up-regulated by Hemin. Conclusions:Those consequences indicated that NO might work downstream in Hemin-heightened anthocyanin accumulation in radish sprouts.

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Calcium Positively Mediates Blue Light-Induced Anthocyanin Accumulation in Hypocotyl of Soybean Sprouts

Frontiers in Plant Science ◽

10.3389/fpls.2021.662091 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gang Hu ◽

Xiaomeng Yue ◽

Jinxue Song ◽

Guipei Xing ◽

Jun Chen ◽

...

Keyword(s):

Blue Light ◽

Anthocyanin Biosynthesis ◽

Calcium Supplementation ◽

Distribution Patterns ◽

Anthocyanin Synthesis ◽

Regulation Mechanism ◽

Anthocyanin Content ◽

Anthocyanin Accumulation ◽

Soybean Sprouts ◽

Expression Of Genes

Soybean sprouts are a flavorful microgreen that can be eaten all year round and are widely favored in Southeast Asia. In this study, the regulatory mechanism of calcium on anthocyanin biosynthesis in soybean sprouts under blue light was investigated. The results showed that blue light, with a short wavelength, effectively induced anthocyanin accumulation in the hypocotyl of soybean sprout cultivar “Dongnong 690.” Calcium supplementation further enhanced anthocyanin content, which was obviously inhibited by LaCl3 and neomycin treatment. Moreover, exogenous calcium changed the metabolism of anthocyanins, and seven anthocyanin compounds were detected. The trend of calcium fluorescence intensity in hypocotyl cells, as well as that of the inositol 1,4,5-trisphosphate and calmodulin content, was consistent with that of anthocyanins content. Specific spatial distribution patterns of calcium antimonate precipitation were observed in the ultrastructure of hypocotyl cells under different conditions. Furthermore, calcium application upregulated the expression of genes related to anthocyanin biosynthesis, and calcium inhibitors suppressed these genes. Finally, transcriptomics was performed to gain global insights into the molecular regulation mechanism of calcium-associated anthocyanin production. Genes from the flavonoid biosynthesis pathway were distinctly enriched among the differentially expressed genes, and weighted gene co-expression network analysis showed that two MYBs were related to the accumulation of anthocyanins. These results indicated that calcium released from apoplast and intracellular stores in specific spatial-temporal features promote blue light-induced anthocyanin accumulation by upregulation of the expression of genes related to anthocyanin synthesis of “Dongnong 690” hypocotyl. The findings deepen the understanding of the calcium regulation mechanism of blue light-induced anthocyanin accumulation in soybean sprouts, which will help growers produce high-quality foods beneficial for human health.

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Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

10.21203/rs.3.rs-36919/v3 ◽

2020 ◽

Author(s):

Shan Feng ◽

Hongcheng Fang ◽

Xia Liu ◽

Yuhui Dong ◽

Qingpeng Wang ◽

...

Keyword(s):

Disease Resistance ◽

Plant Disease Resistance ◽

Molecular Mechanisms ◽

Target Genes ◽

Colletotrichum Gloeosporioides ◽

Juglans Regia ◽

Bioinformatic Analysis ◽

Genome Wide ◽

Phenylpropanoid Biosynthesis ◽

Non Coding Rnas

Abstract Background: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.Results: The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.Conclusions: The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

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Exploring the Roles of Fecundity-related mRNAs and Long Non-coding RNAs in the Adrenal Glands of Small-tailed Han Sheep

10.21203/rs.2.15698/v3 ◽

2020 ◽

Author(s):

Qing Xia ◽

Qiuling Li ◽

Shangquan Gan ◽

Xiaofei Guo ◽

Xiaosheng Zhang ◽

...

Keyword(s):

Adrenal Gland ◽

Signaling Pathways ◽

Transforming Growth Factor Beta ◽

Molecular Mechanisms ◽

Target Genes ◽

Transforming Growth Factor ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Gene Expressions ◽

Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between FecB ++ (WW) and FecB BB (MM) sheep in the follicular and luteal phases and key lncRNAs and genes associated with reproduction were identified. Results In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 30 differentially expressed lncRNAs and 210 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Key lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761 , XLOC_357966 , 105614839 and XLOC_212877 targeting CREB1 , PER3 , SMAD1 and TGFBR2 , respectively, appear to play key regulatory roles. Conclusion These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

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