scholarly journals Elucidation of molecular mechanisms of flower form development in tree peony ( Paeonia suffriticosa ) through comparative transcriptome analysis of floral parts

2019 ◽  
Author(s):  
Jiuxing Lu ◽  
Yun Zheng ◽  
Haoning Wang ◽  
Zheng Wang ◽  
Yonghua Li ◽  
...  
Keyword(s):  
Woody Plants ◽  
Molecular Mechanisms ◽  
High Expression ◽  
Limited Information ◽  
Mads Box ◽  
Mads Box Genes ◽  
Tree Peony ◽  
Expression Levels ◽  
Key Genes ◽  
Flower Form

Abstract Background: Tree peony (Paeonia suffruticasa) is an economically, medicinally ornamentally important woody flowering woody plants in East Asia and is a common also ornamental shrub in Europe and North America. It is well known and prized for their beautiful flowers in many different forms. Samen petalody has been shown to be the most effective way to modify flower forms. However, there is limited information on the molecular mechanisms of stamen petalody and flower form formation in tree peony.Results: In this study, RNA sequencing was used to assemble and annotate the unigenes in the tree peony to identify the critical genes related to flower parts formation and verify the key genes in different flower forms of tree peony cultivar. A total of 76,007 high quality unigenes were assembled and 30,505 were successfully annotated. A total of 1,833 TFs were identified in our study, among them 16 MADS-box genes were found and characterized. Six key genes were selected to verity their functions in stamen petalody. AG and SEP showed high expression level in carpals and sepals separately both in stamen petalody group and non-stamen petalody groups. PI and AP3 showed high expression levels in inter-petals in stamen petalody groups than in staments in non-stamen petalody.Conclusion: Sixteen MADS-box genes were identified for the first time in tree peony through RNA-seq method. We identified six key genes based on their differential expression levels in different flower parts. These six key genes represented all categories in the ABCDE model to verify the functions in stamen petalody. PI and AP3 were verified to likely play important roles in regulating stamen petalody in tree peony. Our study has helped establish the flower development model in tree peony, identified key molecular mechanisms in the development of different flower forms, and provided valuable information in improving genetic diversity of tree peony and many other woody plants.

scholarly journals Elucidation of molecular mechanisms of flower form development in tree peony ( Paeonia suffriticosa ) through comparative transcriptome analysis of floral parts

2020 ◽  
Author(s):  
Jiuxing Lu ◽  
Yun Zheng ◽  
Haoning Wang ◽  
Zheng Wang ◽  
Yonghua Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Flowering Plant ◽  
Limited Information ◽  
Mads Box ◽  
Mads Box Genes ◽  
Tree Peony ◽  
Expression Levels ◽  
Key Genes ◽  
Flower Form ◽  
Form Development

Abstract Background: Tree peony ( Paeonia suffruticasa ) is an economically, medicinally and ornamentally important woody flowering plant in East Asia. It is also a common ornamental shrub in Europe and North America. They are well known and prized for their beautiful flowers in many different shapes. Stamen petalody has been shown to be the most effective way to modify flower shapes. However, there is limited information on the molecular mechanisms of stamen petalody and flower shape formation in tree peony. Results: In this study, RNA sequencing was used to assemble and annotate the unigenes in tree peony to identify the critical genes related to flower parts formation and verify the key genes in different flower shapes of tree peony cultivars. A total of 76,007 high quality unigenes were assembled and 30,505 were successfully annotated. A total of 1,833 transcription factors (TFs) were identified in our study, among them 16 MADS-box genes were found and characterized. Six key genes were selected to verify their functions in stamen petalody. AG and SEP showed high expression level in carpels and sepals separately both in stamen petalody and non-stamen petalody groups. PI and AP3 s howed higher expression levels of inter-petals in the stamen petalody group, compared to stamens of non-stamen petalody. Conclusion: S ixteen MADS-box genes were identified in tree peony through RNA-seq. We identified six key genes based on their differential expression levels in different flower parts. These six key genes represented all categories in the ABCDE model to verify the functions in stamen petalody. We speculate that PI and AP3 may trigger the stamen petalody in tree peony. Our study has helped establish the flower development model in tree peony, to identify key molecular mechanisms in the development of different flower shapes, and to provide valuable information for improving the genetic diversity of tree peony and many other woody plants.

Cloning and quantification of expression levels of two MADS-box genes from Momordica charantia

2008 ◽  
Vol 52 (2) ◽  
pp. 222-230 ◽  
Author(s):  
S. M. Peng ◽  
T. Luo ◽  
J. Y. Zhou ◽  
B. Niu ◽  
N. F. Lei ◽  
...  
Keyword(s):  
Momordica Charantia ◽  
Mads Box ◽  
Mads Box Genes ◽  
Expression Levels

Identification and quantification of expression levels of three FRUITFULL-like MADS-box genes from the orchid Dendrobium thyrsiflorum (Reichb. f.)

Plant Science ◽  
2005 ◽  
Vol 169 (3) ◽  
pp. 579-586 ◽  
Author(s):  
Martin Skipper ◽  
Kim B. Pedersen ◽  
Louise B. Johansen ◽  
Signe Frederiksen ◽  
Vivian F. Irish ◽  
...  
Keyword(s):  
Mads Box ◽  
Mads Box Genes ◽  
Expression Levels ◽  
Identification And Quantification

scholarly journals Identification of potential biomarkers and candidate small molecule drugs in glioblastoma

2020 ◽  
Author(s):  
Wei-cheng Lu ◽  
Hui Xie ◽  
Ce Yuan ◽  
Jin-jiang Li ◽  
Zhao-yang Li ◽  
...  
Keyword(s):  
Protein Expression ◽  
Small Molecule ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Integrated Analysis ◽  
Hub Genes ◽  
Expression Levels ◽  
Small Molecule Drugs ◽  
Key Genes

Abstract Background and aims:Glioblastoma (GBM) is a common and aggressive primary brain tumor, and the prognosis for GBM patients remains poor. This study aimed to identify the key genes associated with the development of GBM and provide new diagnostic and therapies for GBM. Methods:Three microarray datasets (GSE111260, GSE103227, and GSE104267) were selected from Gene Expression Omnibus (GEO) database for integrated analysis. The differential expressed genes (DEGs) between GBM and normal tissues were identified. Then, prognosis-related DEGs were screened by survival analysis, followed by functional enrichment analysis. The protein-protein interaction (PPI) network was constructed to explore the hub genes associated with GBM. The mRNA and protein expression levels of hub genes were respectively validated in silico using The Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) databases. Subsequently, the small molecule drugs of GBM were predicted by using Connectivity Map (CMAP) database. Results:A total of 78 prognosis-related DEGs were identified, of which10 hub genes with higher degree were obtained by PPI analysis. The mRNA expression and protein expression levels of CETN2, MKI67, ARL13B, and SETDB1 were overexpressed in GBM tissues, while the expression levels of CALN1, ELAVL3, ADCY3, SYN2, SLC12A5, and SOD1 were down-regulated in GBM tissues. Additionally, these genes were significantly associated with the prognosis of GBM. We eventually predicted the 10 most vital small molecule drugs, which potentially imitate or reverse GBM carcinogenic status. Cycloserine and 11-deoxy-16,16-dimethylprostaglandin E2 might be considered as potential therapeutic drugs of GBM. Conclusions:Our study provided 10 key genes for diagnosis, prognosis, and therapy for GBM. These findings might contribute to a better comprehension of molecular mechanisms of GBM development, and provide new perspective for further GBM research. However, specific regulatory mechanism of these genes needed further elaboration.

scholarly journals Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

2021 ◽  
Vol 12 ◽  
Author(s):  
Anna V. Shchennikova ◽  
Alexey V. Beletsky ◽  
Mikhail A. Filyushin ◽  
Maria A. Slugina ◽  
Eugeny V. Gruzdev ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Mads Box ◽  
Mads Box Genes ◽  
Evolutionary Origins ◽  
Novel Structure ◽  
Genes Encoding

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

scholarly journals Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Lyne Jossé ◽  
Tarun Singh ◽  
Tobias von der Haar
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Codon Usage ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Selective Pressure ◽  
Recombinant Protein Expression ◽  
High Expression ◽  
Expression Levels ◽  
Optimal Codon

AbstractOne of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. However, when high expression levels are not required, optimal codon usage is surprisingly and strongly selected against. We show that this selection acts at the level of protein synthesis, and we exclude a number of molecular mechanisms as the source for this negative selective pressure including nutrient and ribosome limitations and proteotoxicity effects. These findings inform our understanding of the evolution of codon usage bias, as well as the design of recombinant protein expression systems.

scholarly journals Constitutive Expression of an Apple FLC3-like Gene Promotes Flowering in Transgenic Blueberry under Nonchilling Conditions

2019 ◽  
Vol 20 (11) ◽  
pp. 2775 ◽  
Author(s):  
Xiaojuan Zong ◽  
Yugang Zhang ◽  
Aaron Walworth ◽  
Elise M. Tomaszewski ◽  
Pete Callow ◽  
...  
Keyword(s):  
Woody Plants ◽  
Reverse Genetics ◽  
Opposite Effect ◽  
Constitutive Expression ◽  
Vaccinium Corymbosum ◽  
Mads Box ◽  
Mads Box Genes ◽  
Transgenic Expression ◽  
Future Studies ◽  
Mads Box Gene

MADS-box transcription factors FLOWERING LOCUS C (FLC) and APETALA1 (AP1)/CAULIFLOWER (CAL) have an opposite effect in vernalization-regulated flowering in Arabidopsis. In woody plants, a functional FLC-like gene has not been verified through reverse genetics. To reveal chilling-regulated flowering mechanisms in woody fruit crops, we conducted phylogenetic analysis of the annotated FLC-like proteins of apple and found that these proteins are grouped more closely to Arabidopsis AP1 than the FLC group. An FLC3-like MADS-box gene from columnar apple trees (Malus domestica) (MdFLC3-like) was cloned for functional analysis through a constitutive transgenic expression. The MdFLC3-like shows 88% identity to pear’s FLC-like genes and 82% identity to blueberry’s CAL1 gene (VcCAL1). When constitutively expressed in a highbush blueberry (Vaccinium corymbosum L.) cultivar ‘Legacy’, the MdFLC3-like induced expressions of orthologues of three MADS-box genes, including APETALA1, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, and CAL1. As a consequence, in contrast to the anticipated late flowering associated with an overexpressed FLC-like, the MdFLC3-like promoted flowering of transgenic blueberry plants under nonchilling conditions where nontransgenic ‘Legacy’ plants could not flower. Thus, the constitutively expressed MdFLC3-like in transgenic blueberries functioned likely as a blueberry’s VcCAL1. The results are anticipated to facilitate future studies for revealing chilling-mediated flowering mechanisms in woody plants.

scholarly journals A MADS-Box Gene CiMADS43 Is Involved in Citrus Flowering and Leaf Development through Interaction with CiAGL9

2021 ◽  
Vol 22 (10) ◽  
pp. 5205
Author(s):  
Li-Xia Ye ◽  
Jin-Xia Zhang ◽  
Xiao-Jin Hou ◽  
Mei-Qi Qiu ◽  
Wen-Feng Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Regulation Mechanism ◽  
Mads Box ◽  
Mads Box Genes ◽  
Vegetative Development ◽  
Protein Protein Interaction ◽  
Arabidopsis Protein ◽  
Seasonal Flowering ◽  
Mads Box Gene ◽  
Pollen Formation

MADS-box genes are involved in various developmental processes including vegetative development, flower architecture, flowering, pollen formation, seed and fruit development. However, the function of most MADS-box genes and their regulation mechanism are still unclear in woody plants compared with model plants. In this study, a MADS-box gene (CiMADS43) was identified in citrus. Phylogenetic and sequence analysis showed that CiMADS43 is a GOA-like Bsister MADS-box gene. It was localized in the nucleus and as a transcriptional activator. Overexpression of CiMADS43 promoted early flowering and leaves curling in transgenic Arabidopsis. Besides, overexpression or knockout of CiMADS43 also showed leaf curl phenotype in citrus similar to that of CiMADS43 overexpressed in Arabidopsis. Protein–protein interaction found that a SEPALLATA (SEP)-like protein (CiAGL9) interacted with CiMADS43 protein. Interestingly, CiAGL9 also can bind to the CiMADS43 promoter and promote its transcription. Expression analysis also showed that these two genes were closely related to seasonal flowering and the development of the leaf in citrus. Our findings revealed the multifunctional roles of CiMADS43 in the vegetative and reproductive development of citrus. These results will facilitate our understanding of the evolution and molecular mechanisms of MADS-box genes in citrus.

scholarly journals Genome-Wide Identification MIKC-Type MADS-Box Gene Family and Their Roles during Development of Floral Buds in Wheel Wingnut (Cyclocarya paliurus)

2021 ◽  
Vol 22 (18) ◽  
pp. 10128
Author(s):  
Yinquan Qu ◽  
Weilong Kong ◽  
Qian Wang ◽  
Xiangxiang Fu
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Expression Profile ◽  
Mads Box ◽  
Mads Box Genes ◽  
Cyclocarya Paliurus ◽  
Expression Levels ◽  
Floral Buds ◽  
Genome Wide ◽  
Mads Box Gene

MADS-box transcription factors (TFs) have fundamental roles in regulating floral organ formation and flowering time in flowering plants. In order to understand the function of MIKC-type MADS-box family genes in Cyclocarya paliurus (Batal.) Iljinskaja, we first implemented a genome-wide analysis of MIKC-type MADS-box genes in C. paliurus. Here, the phylogenetic relationships, chromosome location, conserved motif, gene structure, promoter region, and gene expression profile were analyzed. The results showed that 45 MIKC-type MADS-box were divided into 14 subfamilies: BS (3), AGL12 (1), AP3-PI (3), MIKC* (3), AGL15 (3), SVP (5), AGL17 (2), AG (3), TM8 (1), AGL6 (2), SEP (5), AP1-FUL (6), SOC1 (7), and FLC (1). The 43 MIKC-type MADS-box genes were distributed unevenly in 14 chromosomes, but two members were mapped on unanchored scaffolds. Gene structures were varied in the same gene family or subfamily, but conserved motifs shared similar distributions and sequences. The element analysis in promoters’ regions revealed that MIKC-type MADS-box family genes were associated with light, phytohormone, and temperature responsiveness, which may play important roles in floral development and differentiation. The expression profile showed that most MIKC-type MADS-box genes were differentially expressed in six tissues (specifically expressed in floral buds), and the expression patterns were also visibly varied in the same subfamily. CpaF1st24796 and CpaF1st23405, belonging to AP3-PI and SEP subfamilies, exhibited the high expression levels in PA-M and PG-F, respectively, indicating their functions in presenting heterodichogamy. We further verified the MIKC-type MADS-box gene expression levels on the basis of transcriptome and qRT-PCR analysis. This study would provide a theoretical basis for classification, cloning, and regulation of flowering mechanism of MIKC-type MADS-box genes in C. paliurus.

scholarly journals Expression Profiles Reveal Involvement of VEGF, IGF1, BIRC5, and MMP1 in Vulvar Carcinogenesis

2021 ◽  
Vol 20 ◽  
pp. 153303382110049
Author(s):  
Tao Zhang ◽  
Qin Liu ◽  
Minghua Yu ◽  
Yibing Lan ◽  
Jianghong Zhou
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Clinical Stage ◽  
Clinicopathological Characteristics ◽  
Gene Expression Omnibus ◽  
Expression Levels ◽  
Key Genes ◽  
Well Differentiated ◽  
New Biomarkers

Objective: The objective of this study was to identify key genes and shed light on the underlying molecular mechanisms of vulvar squamous cell carcinoma (VSCC). Methods: Bioinformatic software was utilized for the identification and characterization of key differentially expressed genes (DEGs) from microarrays GSE63678 and GSE38228, which contain VSCC and normal vulvar tissue data. These microarrays were obtained from Gene Expression Omnibus (GEO). Immunohistochemical assays (55 VSCC and 50 normal vulvar tissues) were utilized to validate the expression of VEGF, IGF1, BIRC5, and MMP1 screened from the identified DEGs. SPSS 18.0 software was used for statistical analyses of the relationships between IGF1, BIRC5, VEGF, MMP1 expression levels and patient clinicopathological characteristics. Results: A total of 141 DEGs were identified, among which 18 genes were closely correlated with the biological characteristics of VSCC. Four of the 18 genes ( VEGF, IGF1, BIRC5, and MMP1) screened from the GEO database were markedly enriched in pathways in cancer ( P < 0.05), and could be considered key genes in VSCC based on KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis in DAVID (Database for Annotation, Visualization and Integrated Discovery).The expression levels of these 4 hub genes, determined by immunohistochemical assays, were consistent with the bioinformatics results. Higher expression of IGF1 showed significant association with well-differentiated carcinomas ( P = 0.017). BIRC5 expression levels showed a positive correlation with clinical stage ( P = 0.039); compared with those in menopause for over 10 years, patients in menopause for less than 10 years at the time of diagnosis tended to have significantly higher expression of BIRC5 ( P = 0.003). VEGF and MMP1 expression levels were not correlated with any of the tested clinicopathological characteristics. Conclusion: VEGF, IGF1, BIRC5, and MMP1 were identified as being associated with VSCC using integrated bioinformatic methods, which may provide important insights into the pathogenesis of this disease and help to identify new biomarkers.

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