scholarly journals Important Roles of Key Genes and Transcription Factors in Flower Color Differences of Nicotiana alata

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1976
Author(s):  
Yalin Zheng ◽  
Yudong Chen ◽  
Zhiguo Liu ◽  
Hui Wu ◽  
Fangchan Jiao ◽  
...  
Keyword(s):  
Differential Expression ◽  
Anthocyanin Biosynthesis ◽  
Chlorophyll Biosynthesis ◽  
Enrichment Analysis ◽  
Flower Color ◽  
Nicotiana Alata ◽  
Biosynthesis Pathway ◽  
Color Differences ◽  
Differential Expression Genes ◽  
Horticultural Plant

Nicotiana alata is an ornamental horticultural plant with a variety of flower colors and a long flowering period. The genes in four different colored N. alata (white, purple, red, and lemon green) were analyzed to explain the differences in flower color using transcriptomes. A total of 32 differential expression genes in the chlorophyll biosynthesis pathway and 41 in the anthocyanin biosynthesis pathway were identified. The enrichment analysis showed that the chlorophyll biosynthesis pathway and anthocyanin biosynthesis pathway play critical roles in the color differences of N. alata. The HEMA of the chlorophyll biosynthesis pathway was up-regulated in lemon green flowers. Compared with white flowers, in the red and purple flowers, F3H, F3′5′H and DFR were significantly up-regulated, while FLS was significantly down-regulated. Seventeen differential expression genes homologous to transcription factor coding genes were obtained, and the homologues of HY5, MYB12, AN1 and AN4 were also involved in flower color differences. The discovery of these candidate genes related to flower color differences is significant for further research on the flower colors formation mechanism and color improvements of N. alata.

scholarly journals Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

2021 ◽  
Author(s):  
Yu Ding ◽  
Ding-Hai Yang ◽  
Ma-Yin Wang ◽  
Dai-Cheng Hao ◽  
Wei-Shi Li ◽  
...  
Keyword(s):  
Differential Expression ◽  
Economic Value ◽  
Flower Color ◽  
Rna Seq ◽  
Transcription Level ◽  
Color Formation ◽  
Pathway Enrichment ◽  
Differential Expression Genes ◽  
Important Position ◽  
Transcriptome Level

Abstract Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

scholarly journals Exploring the Molecular Mechanism of Blue Flower Color Formation in Hydrangea macrophylla cv. “Forever Summer”

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiqing Peng ◽  
Xujie Dong ◽  
Chao Xue ◽  
Zhiming Liu ◽  
Fuxiang Cao
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanism ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Flower Color ◽  
Anthocyanin Synthesis ◽  
Blue Flower ◽  
Biosynthesis Pathway ◽  
Color Formation ◽  
Hydrangea Macrophylla

Hydrangea macrophylla has a large inflorescence and rich colors, which has made it one of the most popular ornamental flowers worldwide. Thus far, the molecular mechanism of flower color formation in H. macrophylla flowers is unknown. By comparing the pigment content and transcriptome data of the bud period (FSF1), discoloration period (FSF2) and full-bloom stage (FSF3) of infertile blue flowers of H. macrophylla cv. “Forever Summer,” we found that genes associated with anthocyanin production were most associated with the formation of blue infertile flowers throughout development. The anthocyanin biosynthesis pathway is the main metabolic pathway associated with flower color formation, and the carotenoid biosynthesis pathway appeared to have almost no contribution to flower color. There was no competition between the flavonoid and flavonol and anthocyanin biosynthesis pathways for their substrate. At FSF1, the key genes CHS and CHI in the flavonoid biosynthesis pathway were up-regulated, underlying the accumulation of a substrate for anthocyanin synthesis. By FSF3, the downstream genes F3H, C3′5′H, CYP75B1, DFR, and ANS in the anthocyanin biosynthesis pathway were almost all up-regulated, likely promoting the synthesis and accumulation of anthocyanins and inducing the color change of infertile flowers. By analyzing protein–protein interaction networks and co-expression of transcription factors as well as differentially expressed structural genes related to anthocyanin synthesis, we identified negatively regulated transcription factors such as WER-like, MYB114, and WDR68. Their site of action may be the key gene DFR in the anthocyanin biosynthesis pathway. The potential regulatory mechanism of flower color formation may be that WER-like, MYB114, and WDR68 inhibit or promote the synthesis of anthocyanins by negatively regulating the expression of DFR. These results provide an important basis for studying the infertile flower color formation mechanism in H. macrophylla and the development of new cultivars with other colors.

Screening, cloning and sequence analysis of the differential expression genes in Longissimus dorsi of Yanbian Yellow Cattle

2011 ◽  
Vol 33 (11) ◽  
pp. 1219-1224 ◽  
Author(s):  
Wan-Nian TIAN ◽  
Shou-Fa ZHANG ◽  
Xiang-Zi LI ◽  
Qing-Shan GAO ◽  
Xin JIN ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Differential Expression ◽  
Longissimus Dorsi ◽  
Yellow Cattle ◽  
Differential Expression Genes

Identifying Breast Cancer-induced gene perturbations and its application in guiding drug repurposing

2020 ◽  
Vol 15 ◽  
Author(s):  
Jujuan Zhuang ◽  
Shuang Dai ◽  
Lijun Zhang ◽  
Pan Gao ◽  
Yingmin Han ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Enrichment Analysis ◽  
Cancer Tissue ◽  
Connectivity Analysis ◽  
Cancer Drugs ◽  
Normal Tissues ◽  
Differential Gene ◽  
Differential Modules ◽  
Differential Connectivity

Background: Breast cancer is a complex disease with high prevalence in women, the molecular mechanisms of which are still unclear at present. Most transcriptomic studies on breast cancer focus on differential expression of each gene between tumor and the adjacent normal tissues, while the other perturbations induced by breast cancer including the gene regulation variations, the changes of gene modules and the pathways, which might be critical to the diagnosis, treatment and prognosis of breast cancer are more or less ignored. Objective: We presented a complete process to study breast cancer from multiple perspectives, including differential expression analysis, constructing gene co-expression networks, modular differential connectivity analysis, differential gene connectivity analysis, gene function enrichment analysis key driver analysis. In addition, we prioritized the related anti-cancer drugs based on enrichment analysis between differential expression genes and drug perturbation signatures. Methods: The RNA expression profiles of 1109 breast cancer tissue and 113 non-tumor tissues were downloaded from The Cancer Genome Atlas (TCGA) database. Differential expression of RNAs was identified using the “DESeq2” bioconductor package in R, and gene co-expression networks was constructed using the weighted gene co-expression network analysis (WGCNA). To compare the module changes and gene co-expression variations between tumor and the adjacent normal tissues, modular differential connectivity (MDC) analysis and differential gene connectivity analysis (DGCA) were performed. Results: Top differential genes like MMP11 and COL10A1 were known to be associated with breast cancer. And we found 23 modules in the tumor network had significantly different co-expression patterns. The top differential modules were enriched in Goterms related to breast cancer like MHC protein complex, leukocyte activation, regulation of defense response and so on. In addition, key genes like UBE2T driving the top differential modules were significantly correlated with the patients’ survival. Finally, we predicted some potential breast cancer drugs, such as Eribulin, Taxane, Cisplatin and Oxaliplatin. Conclusion: As an indication, this framework might be useful in understanding the molecular pathogenesis of diseases like breast cancer and inferring useful drugs for personalized medication

scholarly journals Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Xueqiang Cui ◽  
Jieling Deng ◽  
Changyan Huang ◽  
Xuan Tang ◽  
Xianmin Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Transcriptome Profiling ◽  
Flower Color ◽  
Flower Bud ◽  
Color Formation ◽  
Color Development ◽  
Purple Coloration ◽  
Purple Color

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

scholarly journals Transcriptome analyses reveal anthocyanin biosynthesis in eggplants

2018 ◽  
Author(s):  
Xi Ou Xiao ◽  
Wen qiu Lin ◽  
Ke Li ◽  
Xue Feng Feng ◽  
Hui Jin ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Negative Regulation ◽  
Anthocyanin Content ◽  
Biosynthesis Pathway ◽  
Rna Seq ◽  
Wild Type ◽  
Rt Pcr ◽  
Total Anthocyanin ◽  
Total Anthocyanin Content ◽  
Cumulative Knowledge

We obtained a white-peel eggplant (L6-5) by EMS mutation in our previous study, whose total anthocyanin content was significantly decreased as compared with that of wild-type (WT). To analyse the anthocyanin biosynthesis mechanism in eggplants, we analysed the eggplant peel by RNA-seq in this study. The transcript results revealed upregulation of 465 genes and downregulation of 525 genes in L6-5 as compared with the WT eggplant. A total of 11 anthocyanin biosynthesis structure genes were significantly downregulated in L6-5 as compared with that in WT. Meanwhile, on the basis of the RT-PCR results of four natural eggplant cultivars, the expression pattern of 11 anthocyanin biosynthesis structure genes was consistent with the anthocyanin content. Thus, we speculated the anthocyanin biosynthesis pathway in eggplant peel. The transcript and RT-PCR results suggested positive regulation of MYB1, MYB108 and TTG8 and negative regulation of bHLH36 in anthocyanin biosynthesis. This study enhanced our cumulative knowledge about anthocyanin biosynthesis in eggplant peels.

scholarly journals Identifying Key MicroRNAs Targeted by Narenmandula in a Rodent Nephropathy Model

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Xiulan Wang ◽  
Chun Chang ◽  
Wenjie Jin ◽  
Arun Arun ◽  
Sudunabuqi Sudunabuqi ◽  
...  
Keyword(s):  
Renal Function ◽  
Differential Expression ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Control Group ◽  
Doxorubicin Hydrochloride ◽  
Treatment Control ◽  
Number Of Genes ◽  
Version 2.0 ◽  
Treatment Control Group

Background. Untreated nephropathy can progress to renal failure. The traditional Mongolian remedy Narenmandula regulates the kidney “yang.” This study aimed to identify key microRNAs (miRNAs) targeted by Narenmandula in a rat model of nephropathy. Methods. Fifteen rats exhibiting normal renal function were randomized to three study arms. Nephropathy was induced in n = 10 rats using doxorubicin hydrochloride, followed by either Narenmandula treatment (treatment group) or no treatment (control group). In n = 5 rats, no doxorubicin was given and renal function remained unchanged (healthy group). Microarray analysis identified miRNAs which were differentially expressed (DE-miRNAs) between groups. Target genes of DE-miRNAs were predicted using miRWalk version 2.0, followed by enrichment analysis using DAVID, and construction of the miRNA coregulatory network using Cytoscape. Results. Nephropathy was successfully induced, with doxorubicin resulting in differential expression of 3645 miRNAs (1324 upregulated and 2321 downregulated). Narenmandula treatment induced differential expression of a total of 159 miRNAs (102 upregulated and 57 downregulated). Upregulated DE-miRNAs (e.g., miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, and miR-30e-5p) and downregulated DE-miRNAs (e.g., miR-330-3p and miR-214-3p) regulated a high number of target genes. Moreover, the miRNA pairs (e.g., miR-195-5p—miR-497-5p, miR-181a-5p—miR-181c-5p, and miR-30e-5p—miR-30a-5p) coregulated a high number of genes. Enrichment analysis indicated functional synergy between miR-30e-5p—miR-30a-3p, miR-34a-5p—miR-30e-5p, miR-30e-5p—miR-195-3p, and miR-30a-3p—miR-195-3p pairs. Conclusion. Narenmandula may modulate doxorubicin-induced nephropathy via targeting miR-497-5p, miR-195-5p, miR-181a-5p, miR-181c-5p, miR-30e-5p, miR-330-3p, miR-214-3p, miR-34a-5p, miR-30a-3p, and miR-30a-5p.

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