De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway

2018 ◽  
Vol 156 ◽  
pp. 201-213 ◽  
Author(s):  
Aaditi B. Deshmukh ◽  
Sagar S. Datir ◽  
Yogesh Bhonde ◽  
Natasha Kelkar ◽  
Pawan Samdani ◽  
...  
Keyword(s):  
De Novo ◽  
Flavonoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Root Transcriptome ◽  
Oroxylum Indicum ◽  
Flavonoid Biosynthesis Pathway

scholarly journals A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Benjamin Jaegle ◽  
Miran Kalle Uroic ◽  
Xu Holtkotte ◽  
Christina Lucas ◽  
Andreas Ole Termath ◽  
...  
Keyword(s):  
Flavonoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Seed Ling ◽  
Flavonoid Biosynthesis Pathway

scholarly journals Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease inLagerstroemia indica

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Xinwang Wang ◽  
Weibing Shi ◽  
Timothy Rinehart
Keyword(s):  
Powdery Mildew ◽  
Plant Defense ◽  
De Novo ◽  
Antioxidant Activities ◽  
Transcript Abundance ◽  
Flavonoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Flavonoid Biosynthesis Pathway

Transcriptome analysis was conducted in two popularLagerstroemiacultivars: “Natchez” (NAT), a white flower and powdery mildew resistant interspecific hybrid and “Carolina Beauty” (CAB), a red flower and powdery mildew susceptibleL. indicacultivar. RNA-seq reads were generated fromErysiphe australianainfected leaves andde novoassembled. A total of 37,035 unigenes from 224,443 assembled contigs in both genotypes were identified. Approximately 85% of these unigenes have known function. Of them, 475 KEGG genes were found significantly different between the two genotypes. Five of the top ten differentially expressed genes (DEGs) involved in the biosynthesis of secondary metabolites (plant defense) and four in flavonoid biosynthesis pathway (antioxidant activities or flower coloration). Furthermore, 5 of the 12 assembled unigenes in benzoxazinoid biosynthesis and 7 of 11 in flavonoid biosynthesis showed higher transcript abundance in NAT. The relative abundance of transcripts for 16 candidate DEGs (9 from CAB and 7 from NAT) detected by qRT-PCR showed general agreement with the abundances of the assembled transcripts in NAT. This study provided the first transcriptome analyses inL. indica. The differential transcript abundance between two genotypes indicates that it is possible to identify candidate genes that are associated with the plant defenses or flower coloration.

scholarly journals De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 133 ◽  
Author(s):  
De-Lin Xu ◽  
Hai Long ◽  
Jun-Jun Liang ◽  
Jie Zhang ◽  
Xin Chen ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Root Transcriptome ◽  
Aegilops Variabilis

scholarly journals Discovery and evaluation of a novel step in the flavonoid biosynthesis pathway regulated by F3H gene using a yeast expression system

2019 ◽  
Author(s):  
Rahmatullah Jan ◽  
Sajjad Asaf ◽  
Sanjita Paudel ◽  
Sangkyu Lee ◽  
Kyung-Min Kim
Keyword(s):  
Western Blotting ◽  
Rice Plant ◽  
Expression System ◽  
Plant Secondary Metabolites ◽  
Flavonoid Biosynthesis ◽  
Yeast Expression ◽  
List Type ◽  
Biosynthesis Pathway ◽  
Yeast Expression System ◽  
Flavonoid Biosynthesis Pathway

AbstractKaempferol and quercetin are the essential plant secondary metabolites that confer huge biological functions in the plant defense system. These metabolites are produced in low quantities in plants, therefore engineering microbial factory is a favorable strategy for the production of these metabolites. In this study, biosynthetic pathways for kaempferol and quercetin were constructed in Saccharomyces cerevisiae using naringenin as a substrate. The results elucidated a novel step for the first time in kaempferol and quercetin biosynthesis directly from naringenin catalyzed by flavonol 3-hydroxylase (F3H). F3H gene from rice was cloned into pRS42K yeast episomal plasmid (YEP) vector using BamH1 and Xho1 restriction enzymes. We analyzed our target gene activity in engineered and in empty strains. The results were confirmed through TLC followed by Western blotting, nuclear magnetic resonance (NMR), and LC-MS. TLC showed positive results on comparing both compounds extracted from the engineered strain with the standard reference. Western blotting confirmed lack of Oryza sativa flavonol 3-hydroxylase (OsF3H) activity in empty strains while high OsF3H expression in engineered strains. NMR spectroscopy confirmed only quercetin, while LCMS-MS results revealed that F3H is responsible for naringenin conversion to both kaempferol and quercetin. These results concluded that rice F3H catalyzes naringenin metabolism via hydroxylation and synthesizes kaempferol and quercetin.HighlightsCurrent study is a discovery of a novel step in flavonoid biosynthesis pathway of rice plant.In this study F3H gene from rice plant was functionally expressed in yeast expression system.Results confirmed that, F3H gene is responsible for the canalization of naringenin and converted into kaempferol and quercetin.The results were confirmed through, western blotting, TLC, HPLC and NMR analysis.

scholarly journals Temporospatial Flavonoids Metabolism Variation in Ginkgo biloba Leaves

2020 ◽  
Vol 11 ◽  
Author(s):  
Ying Guo ◽  
Tongli Wang ◽  
Fang-Fang Fu ◽  
Yousry A. El-Kassaby ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Early Stage ◽  
Sunshine Duration ◽  
Flavonoid Biosynthesis ◽  
Flavonoid Glycosides ◽  
Biosynthesis Pathway ◽  
Flavonoids Biosynthesis ◽  
Flavonoid Biosynthesis Pathway

Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.

scholarly journals Composition of Flavonoids in the Petals of Freesia and Prediction of Four Novel Transcription Factors Involving in Freesia Flavonoid Pathway

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiayi Zhu ◽  
Xueying Guo ◽  
Xin Li ◽  
Dongqin Tang
Keyword(s):  
Transcriptome Sequencing ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Structural Genes ◽  
Flavonoid Pathway ◽  
Illumina Hiseq ◽  
Color Formation ◽  
Flavonoid Biosynthesis Pathway ◽  
Tof Ms

Freesia hybrida is rich in flower colors with beautiful flower shapes and pleasant aroma. Flavonoids are vital to the color formation of its flowers. In this study, five Freesia cultivars with different flower colors were used to study on the level of accumulation of their flavonoids and expression of flavonoid-related genes and further explore new novel transcription factor (TF). Ultra-high-performance liquid chromatography and VION ion mobility quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF-MS) were used to determine the flavonoids. Combined with transcriptome sequencing technology, the molecular mechanism of the flavonoid metabolism difference in Freesia was revealed. A total of 10 anthoxanthin components and 12 anthocyanin components were detected using UPLC-Q-TOF-MS. All six common anthocyanin aglycones in high plants, including cyanidin, delphinidin, petunidin, peonidin, malvidin, and pelargonidin, were detected in Freesia at first time in this study. In orange, yellow, and white cultivars, anthoxanthins gradually decreased with the opening of the petals, while in red and purple cultivars, anthoxanthins first increased and then decreased. No anthocyanin was detected in yellow and white cultivars, while anthocyanins increased with the opening of the petals and reached their maximum at the flowering stage (S3) in other three cultivars. The correlation analysis revealed that the color of Freesia petals was closely related to the composition and content of anthoxanthins and anthocyanins. Petals of five cultivars at S3 were then selected for transcriptome sequencing by using the Illumina Hiseq 4000 platform, and a total of 100,539 unigenes were obtained. There were totally 5,162 differentially expressed genes (DEGs) when the four colored cultivars were compared with the white cultivar at S3. Comparing all DEGs with gene ontology (GO), KEGG, and Pfam databases, it was found that the genes involved in the flavonoid biosynthesis pathway were significantly different. In addition, AP2, WRKY, and bHLH TF families ranked the top three among all differently expressed TFs in all DEGs. Quantitative real-time PCR (qRT-PCR) technology was used to analyze the expression patterns of the structural genes of flavonoid biosynthesis pathway in Freesia. The results showed that metabolic process was affected significantly by structural genes in this pathway, such as CHS1, CHI2, DFR1, ANS1, 3GT1, and FLS1. Cluster analysis was performed by using all annotated WRKY and AP2 TFs and the above structural genes based on their relatively expression. Four novel candidate TFs of WRKY and AP2 family were screened. Their spatiotemporal expression patterns revealed that these four novel TFs may participate in the regulation of the flavonoid biosynthesis, thus controlling its color formation in Freesia petals.

scholarly journals Phenylpropanoid metabolism and pigmentation show divergent patterns between brown color and green color cottons as revealed by metabolic and gene expression analyses

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhonghua LI ◽  
Qian SU ◽  
Mingqi XU ◽  
Jiaqi YOU ◽  
Anam Qadir KHAN ◽  
...  
Keyword(s):  
Fiber Quality ◽  
Flavonoid Biosynthesis ◽  
Cotton Fibers ◽  
Phenylpropanoid Metabolism ◽  
Biosynthesis Pathway ◽  
Genes Encoding ◽  
Colored Cotton ◽  
Different Color ◽  
Naturally Colored Cotton ◽  
Flavonoid Biosynthesis Pathway

Abstract Background Naturally-colored cotton has become increasingly popular because of their natural properties of coloration, UV protection, flame retardant, antibacterial activity and mildew resistance. But poor fiber quality and limited color choices are two key issues that have restricted the cultivation of naturally-colored cotton. To identify the possible pathways participating in fiber pigmentation in naturally-colored cottons, five colored cotton accessions in three different color types (with green, brown and white fiber) were chosen for a comprehensive analysis of phenylpropanoid metabolism during fiber development. Results The expression levels of flavonoid biosynthesis pathway genes in brown cotton fibers were significantly higher than those in white and green cotton fibers. Total flavonoids and proanthocyanidin were higher in brown cotton fibers relative to those in white and green cotton fibers, which suggested that the flavonoid biosynthesis pathway might not participate in the pigmentation of green cotton fibers. Further expression analysis indicated that the genes encoding enzymes for the synthesis of caffeic acid derivatives, lignin and lignan were activated in the developing fibers of the green cotton at 10 and 15 days post-anthesis. Conclusions Our results strengthen the understanding of phenylpropanoid metabolism and pigmentation in green and brown cotton fibers, and may improve the breeding of naturally-colored cottons.

scholarly journals The Basic Helix-Loop-Helix Transcription Factor MYC1 Is Involved in the Regulation of the Flavonoid Biosynthesis Pathway in Grapevine

2010 ◽  
Vol 3 (3) ◽  
pp. 509-523 ◽  
Author(s):  
Imène Hichri ◽  
Simon C. Heppel ◽  
Jérémy Pillet ◽  
Céline Léon ◽  
Stefan Czemmel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Flavonoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Flavonoid Biosynthesis Pathway
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