scholarly journals Comparative transcriptome analysis of hard and tender fruit spines of cucumber to identify genes involved in morphological development of fruit spines

2020 ◽  
Author(s):  
Duo Lv ◽  
Yao Yu ◽  
Liang-Rong Xiong ◽  
Gang Wang ◽  
Jin-An Pang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Developmental Process ◽  
Stage Iii ◽  
Morphological Development ◽  
Wild Type ◽  
Polar Transport ◽  
Cucumber Fruit ◽  
Auxin Polar Transport

Abstract Background: The trichomes of cucumber fruits are also called spines. Cucumber has important commercial value, and its fruit spines represent a classical tissue with which to study the cell division and differentiation mode of multicellular trichomes. Although there have been many studies on the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichome formation remains elusive. In this study, we used a pair of cucumber materials defined as having hard (Ts, wild type) or tender (ts, mutant) spines in a previous study. The whole developmental process of fruit spines was continuously observed by microscopy and SEM. In an attempt to define the developmental stages of fruit spines, transcriptome profiles at different stages were determined to explore the molecular mechanisms underlying the process of spine development. Results: According to significant phenotypic differences, the developmental process of fruit spines was clearly defined as involving four stages. Comparison of transcriptome profiles showed that 803 and 722 genes were upregulated in the stalk (stage II and stage III) and base (stage IV) developmental stages of fruit spines, respectively. Functional analysis of differentially expressed genes (DEGs) showed that for all developmental stages of fruit spines, lipid metabolism, amino acid metabolism, and signal transduction were the most noticeable pathways. However, during the development of the stalk, genes related to auxin polar transport and HD-ZIP transcription factors were significantly upregulated. bHLH transcription factors and cytoskeleton-related genes were significantly upregulated during the development of the base. In addition, stage III was the key point for differentiating between the wild type and mutant. We detected 628 DEGs between the wild type and mutant at this stage. These DEGs are mainly involved in calcium signaling of the cytoskeleton and auxin polar transport, indicating that the main reason for the disorder of the fruit spine developmental pattern in the mutant was a change in cell polarity caused by blocked intercellular signal transmission.Conclusions: Our study defines in great detail the developmental stages of cucumber fruit spines. At the same time, transcriptome profiles are used to present the gene regulatory networks at different developmental stages of cucumber fruit spines. In addition, we analyzed transcriptomic data of a wild type and mutant to elucidate the biological pathways involving C-type lectin receptor-like kinase that regulate the development of fruit spines.

scholarly journals Comparative transcription analysis of hard and tender fruit spines of cucumber to identify genes involved in morphological development of fruit spines

2020 ◽  
Author(s):  
Duo Lv ◽  
Yao Yu ◽  
Liang-Rong Xiong ◽  
Gang Wang ◽  
Jin-An Pang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Mechanism ◽  
Developmental Process ◽  
Expression Patterns ◽  
Gene Families ◽  
Morphological Development ◽  
Wild Type ◽  
Transcription Analysis ◽  
Cucumber Fruit

Abstract Background The trichomes of cucumber on the fruit are also called spines, it not only has important commercial value but also is a classical tissue to study cell division and differentiation mode of multicellular trichomes. Although there have been many researches about the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichomes formation remains elusive. In this study, we took a pair of cucumber materials defined as hard (Ts, wild-type) and tender spines (ts, mutant) in previous study, the whole developmental process of fruit spines was continuously observed by microscope and SEM, in an attempt to define the development stage of fruit spines, transcriptome profiles at different stages was made to explore the molecular mechanism in the process of spines development. Results With significant phenotypic differences, the developmental process of fruit spines was clearly defined as four stages. Comparion of transcriptome profilings showed a total of 2,788 differential expression genes (DEGs) between the wild-type and mutant at different developmental stages of fruit spines, these genes exhibited different expression patterns at different spines developmental stage. Some DEGs related to cell cycle and meristem had also been identified in transcriptome data. By correlating the expression patterns of several transcription factors that have been reported to be involved in the development of spines, we identified some genes that may be involved in the formation of cucumber fruit spines. The cluster analysis of transcription factors revealed that there were 26 transcription factor families that may be involved in the development of fruit spines, among them, the ERF-ERF, bHLH and WAKY family transcription factor gene families were the top three gene families. Conclusions We defined the four stages of fruit spines development and identified a number of genes that may be involved in the development of multicellular trichomes based on comparative transcription. The results provided a step stone for further analysis of the molecular mechanism in the developmental process of multicellular trichomes.

scholarly journals Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal PathogenRhizopus delemar

mSphere ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Poppy C. S. Sephton-Clark ◽  
Jose F. Muñoz ◽  
Elizabeth R. Ballou ◽  
Christina A. Cuomo ◽  
Kerstin Voelz
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Developmental Process ◽  
Fungal Spores ◽  
Hyphal Growth ◽  
Large Shift ◽  
Rhizopus Delemar ◽  
Content Type ◽  
Transcriptional Changes ◽  
Dormant Spore

ABSTRACTRhizopus delemaris an invasive fungal pathogen responsible for the frequently fatal disease mucormycosis. Germination, a crucial mechanism by which infectious spores ofRhizopus delemarcause disease, is a key developmental process that transforms the dormant spore state into a vegetative one. The molecular mechanisms that underpin this transformation may be key to controlling mucormycosis; however, the regulation of germination remains poorly understood. This study describes the phenotypic and transcriptional changes that take place over the course of germination. This process is characterized by four distinct stages: dormancy, isotropic swelling, germ tube emergence, and hyphal growth. Dormant spores are shown to be transcriptionally unique, expressing a subset of transcripts absent in later developmental stages. A large shift in the expression profile is prompted by the initiation of germination, with genes involved in respiration, chitin, cytoskeleton, and actin regulation appearing to be important for this transition. A period of transcriptional consistency can be seen throughout isotropic swelling, before the transcriptional landscape shifts again at the onset of hyphal growth. This study provides a greater understanding of the regulation of germination and highlights processes involved in transformingRhizopus delemarfrom a single-cellular to multicellular organism.IMPORTANCEGermination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore germination occurs in the mucormycetes, identifying processes we may be able to inhibit to help prevent or treat mucormycosis.

scholarly journals Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

2020 ◽  
Author(s):  
Fangfang Li ◽  
Fangming Mei ◽  
Yifang Zhang ◽  
Shumin Li ◽  
Zhensheng Kang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Phylogenetic Relationship ◽  
Developmental Stages ◽  
Land Plants ◽  
Wild Type ◽  
Abiotic Stress Response ◽  
Genome Wide ◽  
Protein Properties ◽  
Relationship Of ◽  
Signaling Components

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

scholarly journals An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple

2019 ◽  
Vol 20 (18) ◽  
pp. 4462 ◽  
Author(s):  
Gaopeng Yuan ◽  
Shuxun Bian ◽  
Xiaolei Han ◽  
Shanshan He ◽  
Kai Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Lignin Biosynthesis ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Proteomics Data ◽  
Absolute Quantitation ◽  
Physiological Disorder ◽  
Golden Delicious

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

scholarly journals Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco

DNA Research ◽  
2020 ◽  
Vol 27 (2) ◽  
Author(s):  
Pingping Liu ◽  
Jie Luo ◽  
Qingxia Zheng ◽  
Qiansi Chen ◽  
Niu Zhai ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Developmental Process ◽  
Pearson Correlation ◽  
Molecular Networks ◽  
Environmental Perturbations ◽  
Carotenoid Metabolism ◽  
Gene Modules

Abstract Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.

scholarly journals The Transcriptional Control of Lymphatic Vascular Development

Physiology ◽  
2011 ◽  
Vol 26 (3) ◽  
pp. 146-155 ◽  
Author(s):  
Mathias Francois ◽  
Natasha L. Harvey ◽  
Benjamin M. Hogan
Keyword(s):  
Transcription Factors ◽  
Cell Fate ◽  
Transcriptional Control ◽  
Molecular Mechanisms ◽  
Developmental Process ◽  
Vascular Development ◽  
Lymphatic Vessels ◽  
Lymphatic Endothelial Cell ◽  
Transcriptional Networks ◽  
Genetic Manipulations

More than 100 years ago, Florence Sabin suggested that lymphatic vessels develop by sprouting from preexisting blood vessels, but it is only over the past decade that the molecular mechanisms underpinning lymphatic vascular development have begun to be elucidated. Genetic manipulations in mice have identified a transcriptional hub comprised of Prox1, CoupTFII, and Sox18 that is essential for lymphatic endothelial cell fate specification. Recent work has identified a number of additional transcription factors that regulate later stages of lymphatic vessel differentiation and maturation. This review highlights recent advances in our understanding of the transcriptional control of lymphatic vascular development and reflects on efforts to better understand the activities of transcriptional networks during this discrete developmental process. Finally, we highlight the transcription factors associated with human lymphatic vascular disorders, demonstrating the importance of understanding how the activity of these key molecules is regulated, with a view toward the development of innovative therapeutic avenues.

scholarly journals Transcriptome and Metabolome Analyses Provide Insights into the Stomium Degeneration Mechanism in Lily

2021 ◽  
Vol 22 (22) ◽  
pp. 12124
Author(s):  
Ling He ◽  
Xinyue Liu ◽  
Ze Wu ◽  
Nianjun Teng
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Cell Structure ◽  
Morphological Characteristics ◽  
Anther Dehiscence ◽  
Strong Correlations ◽  
Horticultural Crop ◽  
Metabolomic Data ◽  
Data Platform

Lily (Lilium spp.) is a widely cultivated horticultural crop that has high ornamental and commercial value but also the serious problem of pollen pollution. However, mechanisms of anther dehiscence in lily remain largely unknown. In this study, the morphological characteristics of the stomium zone (SZ) from different developmental stages of ‘Siberia’ lily anthers were investigated. In addition, transcriptomic and metabolomic data were analyzed to identify the differentially expressed genes (DEGs) and secondary metabolites involved in stomium degeneration. According to morphological observations, SZ lysis occurred when flower buds were 6–8 cm in length and was completed in 9 cm. Transcriptomic analysis identified the genes involved in SZ degeneration, including those associated with hormone signal transduction, cell structure, reactive oxygen species (ROS), and transcription factors. A weighted co-expression network showed strong correlations between transcription factors. In addition, TUNEL (TdT-mediated dUTP nick-end labeling) assays showed that programmed cell death was important during anther SZ degeneration. Jasmonates might also have key roles in anther dehiscence by affecting the expression of the genes involved in pectin lysis, water transport, and cysteine protease. Collectively, the results of this study improve our understanding of anther dehiscence in lily and provide a data platform from which the molecular mechanisms of SZ degeneration can be revealed.

scholarly journals The diverse roles of cytokinins in regulating leaf development

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Wenqi Wu ◽  
Kang Du ◽  
Xiangyang Kang ◽  
Hairong Wei
Keyword(s):  
Leaf Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Developmental Process ◽  
Chlorophyll Synthesis ◽  
Growth Potential ◽  
Sugar Accumulation ◽  
Developmental Processes ◽  
Leaf Formation ◽  
Underlying Mechanisms

AbstractLeaves provide energy for plants, and consequently for animals, through photosynthesis. Despite their important functions, plant leaf developmental processes and their underlying mechanisms have not been well characterized. Here, we provide a holistic description of leaf developmental processes that is centered on cytokinins and their signaling functions. Cytokinins maintain the growth potential (pluripotency) of shoot apical meristems, which provide stem cells for the generation of leaf primordia during the initial stage of leaf formation; cytokinins and auxins, as well as their interaction, determine the phyllotaxis pattern. The activities of cytokinins in various regions of the leaf, especially at the margins, collectively determine the final leaf morphology (e.g., simple or compound). The area of a leaf is generally determined by the number and size of the cells in the leaf. Cytokinins promote cell division and increase cell expansion during the proliferation and expansion stages of leaf cell development, respectively. During leaf senescence, cytokinins reduce sugar accumulation, increase chlorophyll synthesis, and prolong the leaf photosynthetic period. We also briefly describe the roles of other hormones, including auxin and ethylene, during the whole leaf developmental process. In this study, we review the regulatory roles of cytokinins in various leaf developmental stages, with a focus on cytokinin metabolism and signal transduction processes, in order to shed light on the molecular mechanisms underlying leaf development.

scholarly journals Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Fangfang Li ◽  
Fangming Mei ◽  
Yifang Zhang ◽  
Shumin Li ◽  
Zhensheng Kang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Phylogenetic Relationship ◽  
Developmental Stages ◽  
Land Plants ◽  
Wild Type ◽  
Abiotic Stress Response ◽  
Genome Wide ◽  
Protein Properties ◽  
Relationship Of ◽  
Signaling Components

Abstract Background Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

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