The molecular mechanism of transcription factors ABM in regulation of strawberry fruit ripening.
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MYB
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Lycopersicon
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The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking. We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (like ra1, ba1, gt1, tb1, tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways. This network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
Gene regulatory network
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Pollen wall is the most complicated cell wall in plant.It is composed of outer exine and inner intine with the exine further divided into sexine and nexine.The composition of intine layer is generally considered to be same as a plant cell wall which is mainly composed of cellulose.Nexine layer can only be observed under transmission electron microscope.Recent investigation suggested that the major composition of nexine is arabinogalactan proteins (Jia et al., 2015).The sexine layer is composed of sporopollenin which is quite stable and resistant to degradation by enzymes and strong chemical reagents.The sporopollenin deposition determines the pollen wall pattern which is widely used for plant taxonomic classifications.After meiosis, microsporocyte divides into four microspores enwrapped in a tetrad with each microspore further develops into a mature pollen.Materials from tapetum penetrate tetrad wall to deposit on the surface of microspore at late tetrad stage.The pollen wall pattern is determined inside the tetrad (Xu et al., 2016).After microspore release, the pollen wall materials continue deposition to form decorated sexine layer and flat nexine (Zhou et al., 2015).After exine layer occurs, intine layer is gradually formed between exine and microspore plasma membrane.Although the chemical composition of sporopollenin is not exactly known, it is assumed to consist of the heterogeneous materials derived from long-chain fatty acids, oxygenated
Sporopollenin
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This paper reviews the recent advances in the understanding of the fruit ripening process and describes future challenges. Fruit ripening is a complex developmental process which is orchestrated by the expression of ripening-related genes under the control of a network of signaling pathways. In climacteric fruit components responsible for the production of climacteric ethylene have been identified. Less progress has been made on non-climacteric fruit. Great advances have been made in the characterization of transcription factors (ERFs, RIN, etc…) that induce gene expression through the binding to their promoters. Genetic resources, genome sequencing and “omics” tools have been developed bringing a huge amount of data that will help to draw an integrative network of regulatory and signaling pathways responsible for triggering and coordinating the ripening process. The discovery that some ripening events are controlled at the epigenetic level and not in relation with the DNA sequences opens novel perspectives.
Climacteric
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Carbon source
Glycerol kinase
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Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry varieties with enhanced health benefits.Toward this end, we annotated a previously sequenced draft blueberry genome assembly using RNA-Seq data from five stages of berry fruit development and ripening. Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape Vitis vinifera. Comparison of gene models to the PlantCyc database of metabolic pathway enzymes identified candidate genes involved in synthesis of bioactive compounds, including bixin, an apocarotenoid with potential disease-fighting properties, and defense-related cyanogenic glycosides, which are toxic. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up-regulated during fruit ripening. Candidate genes for ethylene, anthocyanin, and 400 other biosynthetic pathways were also identified. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up- and down-regulation of metabolic pathway enzymes and transcriptional regulators. Analysis of RNA-seq alignments identified developmentally regulated alternative splicing, promoter use, and 3' end formation.We report genome sequence, gene models, functional annotations, and RNA-Seq expression data that provide an important new resource enabling high throughput studies in blueberry.
Candidate gene
RNA-Seq
Sequence assembly
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Plant activators are chemical crop protectants that fortify the immune system in plants. Unlike pesticides that target pathogens, plant activators provide durable effects against a broad spectrum of diseases, which have not been overcome by pathogenic microbes. Plant activators are not only useful agrochemicals, but can also help to elucidate the details of the plant immune system. Using an established high-throughput screening procedure, we previously identified 5 compounds, designated as Imprimatins, which prime plant immune response. These compounds increased disease resistance against pathogenic Pseudomonas bacteria in Arabidopsis plants by inhibiting 2 salicylic acid (SA) glucosyltransferases (SAGTs), resulting in accumulation of the phytohormone SA. Here, we report the isolation of 2 additional Imprimatins, B3 and B4, which are structurally similar to Imprimatin B1 and B2. Because these compounds did not have strong inhibitory effects on SAGTs in vitro, they may exert their function after metabolic conversion in vivo.
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Systemic Acquired Resistance
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Plant Immunity
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