Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4′-tetrahydroxy stilbene-2-O-β-d-glucoside

Wang, Zhao; Xia, Wanxia; JieWen, Li; Sheng, Shujing; Lei, Lei; Zhao, Shujing

doi:10.1016/j.gene.2014.06.041

Cited by 16 publications

(7 citation statements)

References 25 publications

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“…In comparison to high-throughput mRNA sequencing (RNA-seq), DGE more accurately detects expression differences in poorly expressed genes and exhibits much less transcript length bias (Hong et al, 2011 ). Thus, DGE has been widely utilized to discriminate differences in transcriptional responses among different tissues and organs in plants in the contexts of biotic and abiotic stress, metabolite biosynthesis, and developmental biology (Tian et al, 2013 ; Wei et al, 2013 ; Zhang et al, 2013 ; Guo et al, 2014 ; Yu et al, 2014 ; Zhao et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling

et al. 2016

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The castor plant (Ricinus communis L.) is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P) and monoecious (JXBM0705M) lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3000 of differentially expressed genes (DEGs) were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, such as auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage) of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that of down-regulation in the small raceme of the mutant. In this study, a large number of DEGs and some suggestions involved in sex expression and reproduction were discovered using DGE analysis, which provides large information and valuable hints for next insights into the molecular mechanism of sex determination. It is useful for other further studies in Ricinus.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling

et al. 2016

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“…However, DGE requires a reference sequence to align the relative small read lengths [ 32 ]. Indeed, performing DGE and RNA-Seq, which provides reference transcriptome, offers an efficient method to identify the candidate genes encoding enzymes involved in the biosynthesis of secondary metabolites in non-model plants [ 42 ].…”

Section: Resultsmentioning

confidence: 99%

Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei

Park

Noh

et al. 2016

BMC Genomics

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BackgroundValeriana fauriei is commonly used in the treatment of cardiovascular diseases in many countries. Several constituents with various pharmacological properties are present in the roots of Valeriana species. Although many researches on V. fauriei have been done since a long time, further studies in the discipline make a limit due to inadequate genomic information. Hence, Illumina HiSeq 2500 system was conducted to obtain the transcriptome data from shoot and root of V. fauriei.ResultsA total of 97,595 unigenes were noticed from 346,771,454 raw reads after preprocessing and assembly. Of these, 47,760 unigens were annotated with Uniprot BLAST hits and mapped to COG, GO and KEGG pathway. Also, 70,013 and 88,827 transcripts were expressed in root and shoot of V. fauriei, respectively. Among the secondary metabolite biosynthesis, terpenoid backbone and phenylpropanoid biosynthesis were large groups, where transcripts was involved. To characterize the molecular basis of terpenoid, carotenoid, and phenylpropanoid biosynthesis, the levels of transcription were determined by qRT-PCR. Also, secondary metabolites content were measured using GC/MS and HPLC analysis for that gene expression correlated with its accumulation respectively between shoot and root of V. fauriei.ConclusionsWe have identified the transcriptome using Illumina HiSeq system in shoot and root of V. fauriei. Also, we have demonstrated gene expressions associated with secondary metabolism such as terpenoid, carotenoid, and phenylpropanoid.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2616-3) contains supplementary material, which is available to authorized users.

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“…Accordingly, we thought that the methods to estimate the DEGs in this study were suitable and the false-positive error might be low. The method DEseq2, EdgeR, or Limma was recently used for DEGs analysis based on the negative binomial distribution model [32,51], but we performed the analysis with the Poisson distribution method previously used in other studies [52,53], followed the qPCR test for some putative target genes in this study. The old method seemed to be suitable for this RNA-seq data, but the new one might be much better.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Suggests Genes Expressed Stage-Independently and Stage–Dependently Modulating the Wing Dimorphism of the Brown Planthopper

Zhang

Liu

2019

Genes

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Wing dimorphism is considered as an adaptive trait of insects. Brown planthoppers (BPHs) Nilaparvata lugens, a serious pest of rice, are either macropterous or brachypterous. Genetic and environmental factors are both likely to control wing morph determination in BPHs, but the hereditary law and genes network are still unknown. Here, we investigated changes in gene expression levels between macropterous and brachypterous BPHs by creating artificially bred morphotype lines. The nearly pure-bred strains of macropterous and brachypterous BPHs were established, and their transcriptomes and gene expression levels were compared. Over ten-thousand differentially expressed genes (DEGs) between macropterous and brachypterous strains were found in the egg, nymph, and adult stages, and the three stages shared 6523 DEGs. The regulation of actin cytoskeleton, focal adhesion, tight junction, and adherens junction pathways were consistently enriched with DEGs across the three stages, whereas insulin signaling pathway, metabolic pathways, vascular smooth muscle contraction, platelet activation, oxytocin signaling pathway, sugar metabolism, and glycolysis/gluconeogenesis were significantly enriched by DEGs in a specific stage. Gene expression trend profiles across three stages were different between the two strains. Eggs, nymphs, and adults from the macropterous strain were distinguishable from the brachypterous based on gene expression levels, and genes that were related to wing morphs were differentially expressed between wing strains or strain × stage. A proposed mode based on genes and environments to modulate the wing dimorphism of BPHs was provided.

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Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4′-tetrahydroxy stilbene-2-O-β-d-glucoside

Cited by 16 publications

References 25 publications

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling

Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling

Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei

Transcriptomic Analysis Suggests Genes Expressed Stage-Independently and Stage–Dependently Modulating the Wing Dimorphism of the Brown Planthopper

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