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.

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 Ocena zmian profilu ekspresji genów kandydujących w podkładkach jabłoni o odmiennym stopniu tolerancji mrozowej

2020 ◽  
pp. 21-32
Author(s):  
Sylwia Keller-Przybyłkowicz ◽  
Mariusz Lewandowski
Keyword(s):  
De Novo ◽  
Rna Seq ◽  
Qrt Pcr

Celem przeprowadzonych badań była identyfikacja genów sprzężonych z cechą mrozoodporności podkładek jabłoni. Ocenę zmian w poziomie ekspresji wyizolowanych genów przeprowadzono metodami RNAseq i qRT-PCR, dla podkładek zróżnicowanych po względem stopnia tolerancji mrozowej: P 66 (tolerancyjna) i M.9 (wrażliwa).W wyniku przeprowadzonych odczytów sekwencji RNA (sekwencjonowanie de novo w systemie Illumina Solid) dla w/w podkładek zidentyfikowano około 167 milionów odczytów unikatowych sekwencji, z których do wstępnych badań weryfikacyjnych wytypowano 15 o zróżnicowanym profilu ekspresji. Sekwencje poddano adnotacji funkcjonalnej. Wytypowane geny kodują: białka strukturalne i integralne błon komórkowych i wakuoli komórkowych, czynników transkrypcyjnych, białek regulujących transport międzykomórkowy i wewnątrzkomórkowy, białek hydrolizujących wiązania C-O i C-N oraz białek wiążących makro- i mikroelementy. Celem weryfikacji typu regulacji sekwencji transkryptomu uzyskanych z sekwencjonowania nowej generacji (NGS), dla tych samych prób przeprowadzono ilościową analizę transkryptu genów (qRT-PCR). Spośród badanych genów, trzy reprezentowały identyczny typ regulacji w badanych układach eksperymentalnych RNA-seq i qRT-PCR. Wytypowane geny stanowią potencjalne sekwencje kandydujące do sporządzenia markerów funkcjonalnych, umożliwiających wczesną selekcję podkładek jabłoni tolerancyjnych na mróz.

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 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 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 Identifying differential isoform abundance with RATs: a universal tool and a warning

2017 ◽  
Author(s):  
Kimon Froussios ◽  
Kira Mourão ◽  
Gordon G. Simpson ◽  
Geoffrey J. Barton ◽  
Nick J. Schurch
Keyword(s):  
Transcript Abundance ◽  
Pcr Primers ◽  
R Package ◽  
Original Study ◽  
Transcript Expression ◽  
Rna Seq ◽  
Qrt Pcr ◽  
False Discovery ◽  
Alignment Free ◽  
Go Terms

AbstractMotivationThe biological importance of changes in gene and transcript expression is well recognised and is reflected by the wide variety of tools available to characterise these changes. Regulation via Differential Transcript Usage (DTU) is emerging as an important phenomenon. Several tools exist for the detection of DTU from read alignment or assembly data, but options for detection of DTU from alignment-free quantifications are limited.ResultsWe present an R package named RATs – (Relative Abundance of Transcripts) – that identifies DTU transcriptome-wide directly from transcript abundance estimations. RATs is agnostic to quantification methods and exploits bootstrapped quantifications, if available, to inform the significance of detected DTU events. RATs contextualises the DTU results and shows good False Discovery performance (median FDR ≤0.05) at all replication levels. We applied RATs to a human RNA-seq dataset associated with idiopathic pulmonary fibrosis with three DTU events validated by qRT-PCR. RATs found all three genes exhibited statistically significant changes in isoform proportions based on Ensembl v60 annotations, but the DTU for two were not reliably reproduced across bootstrapped quantifications. RATs also identified 500 novel DTU events that are enriched for eleven GO terms related to regulation of the response to stimulus, regulation of immune system processes, and symbiosis/parasitism. Repeating this analysis with the Ensembl v87 annotation showed the isoform abundance profiles of two of the three validated DTU genes changed radically. RATs identified 414 novel DTU events that are enriched for five GO terms, none of which are in common with those previously identified. Only 141 of the DTU evens are common between the two analyses, and only 8 are among the 248 reported by the original study. Furthermore, the original qRT-PCR probes no longer match uniquely to their original transcripts, calling into question the interpretation of these data. We suggest parallel full-length isoform sequencing, annotation pre-filtering and sequencing of the transcripts captured by qRT-PCR primers as possible ways to improve the validation of RNA-seq results in future experiments.AvailabilityThe package is available through Github at https://github.com/bartongroup/Rats.

scholarly journals De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway

2022 ◽  
Vol 12 ◽  
Author(s):  
Sang-Ho Kang ◽  
Woo-Haeng Lee ◽  
Joon-Soo Sim ◽  
Niha Thaku ◽  
Saemin Chang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Differential Expression Analysis ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Pharmacological Activities ◽  
Secondary Metabolite Biosynthesis ◽  
Long Read ◽  
Gene Expression Levels

Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.

scholarly journals A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

2017 ◽  
Author(s):  
Mickael Orgeur ◽  
Marvin Martens ◽  
Stefan T. Börno ◽  
Bernd Timmermann ◽  
Delphine Duprez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Draft Genome ◽  
Transcript Abundance ◽  
Accurate Estimation ◽  
Rna Seq ◽  
A Genome ◽  
Transcript Discovery

AbstractThe sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads and the gene annotation that defines gene features must also be taken into account. Partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and ade novotranscriptome assembly. This dual approach enabled us to increase the assignment rate of RNA-seq data by nearly 20% as compared to when using only the chicken reference annotation, contributing therefore to a more accurate estimation of transcript abundance. More generally, this strategy could be applied to any organism with partial genome sequence and/or lacking a manually-curated reference annotation in order to improve the accuracy of gene expression studies.

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.

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