scholarly journals Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11239
Author(s):  
Lanya Shui ◽  
Kaisen Huo ◽  
Yan Chen ◽  
Zilin Zhang ◽  
Yanfang Li ◽  
...  
Keyword(s):  
Illumina Sequencing ◽  
Biosynthetic Pathway ◽  
Differential Expression Analysis ◽  
Flavonoid Biosynthesis ◽  
Pcr Analysis ◽  
Vernonia Amygdalina ◽  
Gene Expressions ◽  
Qrt Pcr ◽  
Flavonoid Biosynthetic Pathway ◽  
Underlying Mechanisms

Background Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown. Methods The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves. Results By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4’ positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthesis. Importantly, integrated metabolome and transcriptome data of V. amygdalina leaves, we systematically constructed a flavonoid biosynthetic pathway with regards to material supplying, flavonoid scaffold biosynthesis, and flavonoid modifications. Our findings contribute significantly to understand the underlying mechanisms of flavonoid biosynthesis in V. amygdalina leaves, and also provide valuable information for potential metabolic engineering.

scholarly journals Small Non-Coding RNAome of Ageing Chondrocytes

2020 ◽  
Vol 21 (16) ◽  
pp. 5675
Author(s):  
Panagiotis Balaskas ◽  
Jonathan A. Green ◽  
Tariq M. Haqqi ◽  
Philip Dyer ◽  
Yalda A. Kharaz ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Differential Expression Analysis ◽  
Cartilage Tissue ◽  
Pcr Analysis ◽  
Small Rna Sequencing ◽  
High Grade ◽  
Human Cartilage ◽  
Fragment Analysis ◽  
Qrt Pcr ◽  
Age Related

Ageing is a leading risk factor predisposing cartilage to osteoarthritis. However, little research has been conducted on the effect of ageing on the expression of small non-coding RNAs (sncRNAs). RNA from young and old chondrocytes from macroscopically normal equine metacarpophalangeal joints was extracted and subjected to small RNA sequencing (RNA-seq). Differential expression analysis was performed in R using package DESeq2. For transfer RNA (tRNA) fragment analysis, tRNA reads were aligned to horse tRNA sequences using Bowtie2 version 2.2.5. Selected microRNA (miRNAs or miRs) and small nucleolar RNA (snoRNA) findings were validated using real-time quantitative Polymerase Chain Reaction (qRT-PCR) in an extended cohort of equine chondrocytes. tRNA fragments were further investigated in low- and high-grade OA human cartilage tissue. In total, 83 sncRNAs were differentially expressed between young and old equine chondrocytes, including miRNAs, snoRNAs, small nuclear RNAs (snRNAs), and tRNAs. qRT-PCR analysis confirmed findings. tRNA fragment analysis revealed that tRNA halves (tiRNAs), tiRNA-5035-GluCTC and tiRNA-5031-GluCTC-1 were reduced in both high grade OA human cartilage and old equine chondrocytes. For the first time, we have measured the effect of ageing on the expression of sncRNAs in equine chondrocytes. Changes were detected in a number of different sncRNA species. This study supports a role for sncRNAs in ageing cartilage and their potential involvement in age-related cartilage diseases.

scholarly journals The Flavonoid Biosynthesis Network in Plants

2021 ◽  
Vol 22 (23) ◽  
pp. 12824
Author(s):  
Weixin Liu ◽  
Yi Feng ◽  
Suhang Yu ◽  
Zhengqi Fan ◽  
Xinlei Li ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Current Knowledge ◽  
Anthocyanin Biosynthesis ◽  
Basic Structure ◽  
Ring Structure ◽  
Flavonoid Biosynthesis ◽  
Comprehensive Overview ◽  
Flavonoid Biosynthetic Pathway ◽  
Intermediate Metabolites ◽  
Important Intermediate

Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.

scholarly journals Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon)

Plants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 614
Author(s):  
Jibiao Fan ◽  
Yanhong Lou ◽  
Haiyan Shi ◽  
Liang Chen ◽  
Liwen Cao
Keyword(s):  
Leaf Senescence ◽  
Plant Hormone ◽  
Bioinformatics Analysis ◽  
Cynodon Dactylon ◽  
Differential Expression Analysis ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Aesthetic Quality ◽  
Qrt Pcr

Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.

scholarly journals Transcriptome and Proteome Profiling of Different Colored Rice Reveals Physiological Dynamics Involved in the Flavonoid Pathway

2019 ◽  
Vol 20 (10) ◽  
pp. 2463 ◽  
Author(s):  
Xiaoqiong Chen ◽  
Yu Tao ◽  
Asif Ali ◽  
Zhenhua Zhuang ◽  
Daiming Guo ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Flavonoid Biosynthesis ◽  
Differentially Expressed ◽  
Potential Candidate ◽  
Rice Cultivars ◽  
Red Rice ◽  
Flavonoid Pathway ◽  
Network Analyses ◽  
Flavonoid Biosynthetic Pathway ◽  
Colored Rice

Black and red rice are rich in both anthocyanin and proanthocyanin content, which belong to a large class of flavonoids derived from a group of phenolic secondary metabolites. However, the molecular pathways and mechanisms underlying the flavonoid biosynthetic pathway are far from clear. Therefore, this study was undertaken to gain insight into physiological factors that are involved in the flavonoid biosynthetic pathway in rice cultivars with red, black, and white colors. RNA sequencing of caryopsis and isobaric tags for relative and absolute quantification (iTRAQ) analyses have generated a nearly complete catalog of mRNA and expressed proteins in different colored rice cultivars. A total of 31,700 genes were identified, of which 3417, 329, and 227 genes were found specific for red, white, and black rice, respectively. A total of 13,996 unique peptides corresponding to 3916 proteins were detected in the proteomes of black, white, and red rice. Coexpression network analyses of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) among the different rice cultivars showed significant differences in photosynthesis and flavonoid biosynthesis pathways. Based on a differential enrichment analysis, 32 genes involved in the flavonoid biosynthesis pathway were detected, out of which only CHI, F3H, ANS, and FLS were detected by iTRAQ. Taken together, the results point to differences in flavonoid biosynthesis pathways among different colored rice cultivars, which may reflect differences in physiological functions. The differences in contents and types of flavonoids among the different colored rice cultivars are related to changes in base sequences of Os06G0162500, Os09G0455500, Os09G0455500, and Os10G0536400. Current findings expand and deepen our understanding of flavonoid biosynthesis and concurrently provides potential candidate genes for improving the nutritional qualities of rice.

scholarly journals NtMYB3, an R2R3-MYB from Narcissus, Regulates Flavonoid Biosynthesis

2019 ◽  
Vol 20 (21) ◽  
pp. 5456 ◽  
Author(s):  
Muhammad Anwar ◽  
Weijun Yu ◽  
Hong Yao ◽  
Ping Zhou ◽  
Andrew C. Allan ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Flavonoid Biosynthesis ◽  
Pcr Analysis ◽  
Wild Type ◽  
Narcissus Tazetta ◽  
Over Expression ◽  
Qrt Pcr ◽  
Red Color ◽  
R2r3 Myb ◽  
R2r3 Myb Transcription Factors

R2R3-MYB transcription factors play important roles in the regulation of plant flavonoid metabolites. In the current study, NtMYB3, a novel R2R3-MYB transcriptional factor isolated from Chinese narcissus (Narcissus tazetta L. var. chinensis), was functionally characterized. Phylogenetic analysis indicated that NtMYB3 belongs to the AtMYB4-like clade, which includes repressor MYBs involved in the regulation of flavonoid biosynthesis. Transient assays showed that NtMYB3 significantly reduced red pigmentation induced by the potato anthocyanin activator StMYB-AN1 in agro-infiltrated leaves of tobacco. Over-expression of NtMYB3 decreased the red color of transgenic tobacco flowers, with qRT-PCR analysis showing that NtMYB3 repressed the expression levels of genes involved in anthocyanin and flavonol biosynthesis. However, the proanthocyanin content in flowers of transgenic tobacco increased as compared to wild type. NtMYB3 showed expression in all examined narcissus tissues; the expression level in basal plates of the bulb was highest. A 968 bp promoter fragment of narcissus FLS (NtFLS) was cloned, and transient expression and dual luciferase assays showed NtMYB3 repressed the promoter activity. These results reveal that NtMYB3 is involved in the regulation of flavonoid biosynthesis in narcissus by repressing the biosynthesis of flavonols, and this leads to proanthocyanin accumulation in the basal plate of narcissus.

scholarly journals Transcriptome-Wide Analysis Reveals Key DEGs in Flower Color Regulation of Hosta plantaginea (Lam.) Aschers

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 31
Author(s):  
Jingying Zhang ◽  
Changhai Sui ◽  
Yanli Wang ◽  
Shuying Liu ◽  
Huimin Liu ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Biosynthetic Pathway ◽  
Flower Color ◽  
White Flower ◽  
Flowering Stage ◽  
Purple Flower ◽  
Late Flowering ◽  
Qrt Pcr ◽  
Flavonoid Biosynthetic Pathway ◽  
Color Regulation

Background: Hosta plantaginea (Lam.) Aschers (HPA), a species in the family Liliaceae, is an important landscaping plant and herbaceous ornamental flower. However, because the flower has only two colors, white and purple, color matching applications are extremely limited. To date, the mechanism underlying flower color regulation remains unclear. Methods: In this study, the transcriptomes of three cultivars—H. plantaginea (HP, white flower), H. Cathayana (HC, purple flower), and H. plantaginea ‘Summer Fragrance’ (HS, purple flower)—at three flowering stages (bud stage, initial stage, and late flowering stage) were sequenced with the Illumina HiSeq 2000 (San Diego, CA, USA). The RNA-Seq results were validated by qRT-PCR of eight differentially expressed genes (DEGs). Then, we further analyzed the relationship between anthocyanidin synthase (ANS), chalcone synthase (CHS), and P450 and the flower color regulation by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG) network and pathway enrichment analyses. The overexpression of CHS and ANS in transgenic tobacco petals was verified using qRT-PCR, and the petal colors associated with the overexpression lines were confirmed using absorbance values. Results: Over 434,349 transcripts were isolated, and 302,832 unigenes were identified. Additionally, through transcriptome comparisons, 2098, 722, and 606 DEGs between the different stages were found for HP, HC, and HS, respectively. Furthermore, GO and KEGG pathway analyses showed that 84 color-related DEGs were enriched in 22 pathways. In particular, the flavonoid biosynthetic pathway, regulated by CHS, ANS, and the cytochrome P450-type monooxygenase gene, was upregulated in both purple flower varieties in the late flowering stage. In contrast, this gene was hardly expressed in the white flower variety, which was verified in the CHS and ANS overexpression transgenic tobacco petals. Conclusions: The results suggest that CHS, ANS, and the cytochrome P450s-regulated flavonoid biosynthetic pathway might play key roles in the regulation of flower color in HPA. These insights into the mechanism of flower color regulation could be used to guide artificial breeding of polychrome varieties of ornamental flowers.

scholarly journals Transcriptomic analysis reveals key transcription factors associated to drought tolerance in a wild papaya (Carica papaya) genotype

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245855
Author(s):  
Humberto Estrella-Maldonado ◽  
Amaranta Girón Ramírez ◽  
Gabriela Fuentes Ortiz ◽  
Santy Peraza-Echeverría ◽  
Octavio Martínez-de la Vega ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Water Deficit ◽  
Carica Papaya ◽  
Differential Expression Analysis ◽  
Transcriptomic Analysis ◽  
Cdna Libraries ◽  
Pcr Analysis ◽  
Water Deficit Stress ◽  
Wild Genotype ◽  
Qrt Pcr

Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown in Mexico. In the present study, plants from a wild Carica papaya genotype and a commercial genotype were subjected to water deficit stress (WDS), and their response was characterized in physiological and molecular terms. The physiological parameters measured (water potential, photosynthesis, Fv/Fm and electrolyte leakage) confirmed that the papaya wild genotype showed better physiological responses than the commercial one when exposed to WDS. Subsequently, RNA-Seq was performed for 4 cDNA libraries in both genotypes (susceptible and tolerant) under well-watered conditions, and when they were subjected to WDS for 14 days. Consistently, differential expression analysis revealed that after 14 days of WDS, the wild tolerant genotype had a higher number of up-regulated genes, and a higher number of transcription factors (TF) that were differentially expressed in response to WDS, than the commercial genotype. Thus, six TF genes (CpHSF, CpMYB, CpNAC, CpNFY-A, CpERF and CpWRKY) were selected for further qRT-PCR analysis as they were highly expressed in response to WDS in the wild papaya genotype. qRT-PCR results confirmed that the wild genotype had higher expression levels (REL) in all 6 TF genes than the commercial genotype. Our transcriptomic analysis should help to unravel candidate genes that may be useful in the development of new drought-tolerant cultivars of this important tropical crop.

scholarly journals Novel bHLH and WD40 transcription factors from turmeric (Curcuma longa L.) as putative regulators of curcumin biosynthesis

2021 ◽  
pp. 20-27
Author(s):  
P. Prashina Mol ◽  
R.S. Aparna ◽  
T.E. Sheeja ◽  
K. Deepa
Keyword(s):  
Transcription Factors ◽  
Biosynthetic Pathway ◽  
Curcuma Longa ◽  
Biologically Active ◽  
Pcr Analysis ◽  
Comparative Transcriptome ◽  
Qrt Pcr ◽  
The Family ◽  
Phenylpropanoid Biosynthesis ◽  
Polymerase Chain

Turmeric, the golden spice belonging to the family Zingiberaceae, is enriched with biologically active curcuminoids composed of curcumin, demethoxycurcumin and bisdemethoxycurcumin. Curcuminoids are phenylpropanoid derivatives, and the biosynthetic pathway is controlled by several transcription factors (TFs). bHLH, WD40 and MYB TFs are the most important TFs regulating phenylpropanoid biosynthesis in plants. Through comparative transcriptome analysis of high and low curcumin germplasm accessions, 20 TFs belonging to the classes bHLH, WD 40, NAC, WRKY and bZIP, which showed differential expression with respect to curcumin, were identified. Among these, two bHLH and one WD40 TFs showed maximum comparative fold change and negative correlation vis-a-vis curcumin content in quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The results of comparative transcriptome and qRT-PCR analyses were in congruence, indicating their putative role as negative regulators.

scholarly journals Whole-transcriptome Analysis Reveals the Promising Bioresource of Total Flavonoid from Bitter-Pit Apples, Especially the Pitted Parts

2020 ◽  
Author(s):  
Xian-Mei YU ◽  
Xiao-Min XUE ◽  
Jin-Zheng WANG ◽  
Pei-Xian NIE ◽  
Ru CHEN ◽  
...  
Keyword(s):  
Chronic Diseases ◽  
Flavonoid Biosynthesis ◽  
Total Flavonoid ◽  
Pcr Analysis ◽  
Total Flavonoid Content ◽  
Rna Seq ◽  
Flavonoid Content ◽  
Qrt Pcr ◽  
Bitter Pit ◽  
Whole Transcriptome

Abstract Background: Apple fruits are rich in flavonoids, and play important roles in human-health protection against chronic diseases. However, pitter pit in apple has affected apple fruit production worldwide. There must be some application values could be exploited from the bitter-pit apples so as to reduce the loss caused by bitter pit.Results: In the present study, the influence of bitter pit on the total flavonoid content and flavonoid biosynthesis in apples was investigated using the aluminum chloride colorimetric method, whole-transcriptome sequencing and qRT-PCR analysis. The results showed that the total flavonoid content in bitter-pit apples (BG), pitted parts (BGBB) and non-pitted parts (JKBF) was 4.28-fold, 4.68-fold and 0.57-fold respectively as that in healthy apples (JKG). By RNA-Seq analysis, 26, 23 and 3 DEGs involved in flavonoid biosynthesis were enriched in JKG vs. BG, JKG vs. BGBB and JKG vs. JKBF comparisons, respectively. Eight DEGs [CYP98A3(1), CYP98A3(2), BADH, DAT, HCT(1), HCT(2), CHI(1) and CHI(2)], were selected to be validated by qRT-PCR analysis, and the consistent expression patterns with RNA-Seq analysis were obtained, the results showed that the 8 DEGs were upregulated in BG and BGBB but downregulated in JKBF when compared with JKG.Conclusions: The flavonoid accumulation and biosynthesis in apples, especially the pitted parts, were stimulated greatly by bitter pit, while depressed slightly in non-pitted parts. The results indicated that the bitter-pit apples, especially the pitted parts, could be used as the promising bioresource of total flavonoid for the therapeutic utilization in human chronic diseases.

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