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丁香实验推荐阅读
Virus-Induced Gene Silencing in Soybean and Common Bean

Plant viral vectors are useful for transient gene expression as well as for downregulation of gene expression via virus-induced gene silencing (VIGS). When used in reverse genetics approaches, VIGS offers a convenient way of transforming genomic information into knowledge of gene fun ...

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Functional Genomic Analysis of Cotton Genes with Agrobacterium-Mediated Virus-Induced Gene Silencing

Cotton (Gossypium spp.) is one of the most agronomically important crops worldwide for its unique textile fiber production and serving as food and feed stock. Molecular breeding and genetic engineering of useful genes into cotton have emerged as advanced approaches to improve cotton yie ...

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Highly Efficient Virus-Induced Gene Silencing in Apple and Soybean by Apple Latent Spherical Virus Vector and Biolistic Inoculation

Virus-induced gene silencing (VIGS) is an effective tool for the analysis of the gene function in plants within a short time. However, in woody fruit tree like apple, some of Solanum crops, and soybean, it is generally difficult to inoculate virus vector by conventional inoculation methods. Here, ...

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VIGS: A Tool to Study Fruit Development in Solanum lycopersicum

A visually traceable system for fast analysis of gene functions based on Fruit-VIGS methodology is described. In our system, the anthocyanin accumulation from purple transgenic tomato lines provides the appropriate background for fruit-specific gene silencing. The tomato Del/R ...

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Virus-Induced Gene Silencing in Strawberry Fruit

Virus-induced gene silencing (VIGS) is a technology that exploits an RNA-mediated antiviral defense mechanism and which has great potential for use in plant reverse genetics. Recently, whole-genome studies and gene sequencing in plants have produced a massive amount of sequence info ...

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A Protocol for VIGS in Arabidopsis Thaliana Using a One-Step TYMV-Derived Vector

Virus-induced gene silencing (VIGS) is an important tool for the analysis of gene function in plants, which can be adapted for high-throughput functional genomics in model plant species such as Arabidopsis thaliana. Here we describe the use of the Turnip yellow mosaic virus (TYMV)-derived v ...

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Virus-Induced Gene Silencing (VIGS) in Plants: An Overview of Target Species and the Virus-Derived Vector Systems

The analysis of gene functions in non-model plant species is often hampered by the fact that stable genetic transformation to downregulate gene expression is laborious and time-consuming, or, for some species, even not achievable. Virus-induced gene silencing (VIGS) can serve as an alter ...

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Rationale for Developing New Virus Vectors to Analyze Gene Function in Grasses Through Virus-Induced Gene Silencing

The exploding availability of genome and EST-based sequences from grasses requires a technology that allows rapid functional analysis of the multitude of genes that these resources provide. There are several techniques available to determine a gene’s function. For gene knockdown st ...

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Virus-Induced Gene Silencing for Rice Using Agroinoculation

Virus-induced gene silencing (VIGS) is a reverse genetics technique that is based on the RNA-mediated defense against viruses in plants. VIGS is a method of gene knockdown triggered by a replicating viral nucleic acid engineered to carry a host gene to be silenced. While there are a number of excell ...

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Utilizing Virus-Induced Gene Silencing for the Functional Characterization of Maize Genes During Infection with the Fungal Pathogen Ustilago maydis

While in dicotyledonous plants virus-induced gene silencing (VIGS) is well established to study plant–pathogen interaction, in monocots only few examples of efficient VIGS have been reported so far. One of the available systems is based on the brome mosaic virus (BMV) which allows gene sile ...

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Virus-Induced Gene Silencing in the Rapid Cycling Columbine Aquilegia coerulea Origami

Aquilegia Origami is an emerging model system for ecology and evolution, which has numerous genetic and genomic tools. Virus-induced gene silencing (VIGS) has been established as an effective approach to study gene function in Aquilegia. In the current protocol, we demonstrate VIGS using ...

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Analysis of Developmental Control Genes Using Virus-Induced Gene Silencing

A consistent challenge in studying the evolution of developmental processes has been the problem of explicitly assessing the function of developmental control genes in diverse species. In recent years, virus-induced gene silencing (VIGS) has proved to be remarkably adaptable and ef ...

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Virus-Induced Gene Silencing of the Alkaloid-Producing Basal Eudicot Model Plant Eschscholzia californica (California Poppy)

Eschscholzia californica (California poppy), a member of the basal eudicot family of the Papaveraceae, is an important species to study alkaloid biosynthesis and the effect of alkaloids on plant metabolism. More recently, it has also been developed as a model system to study the evolution of p ...

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Virus-Induced Gene Silencing Using Artificial miRNAs in Nicotiana benthamiana

Virus-induced gene silencing using artificial microRNAs (MIR VIGS) is a newly developed technique for plant reverse genetic studies. Traditional virus-induced gene silencing (VIGS) assays introduce a large gene fragment, which is expressed and then converted into small RNAs by the e ...

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The Use of VIGS Technology to Study PlantHerbivore Interactions

Plants employ a large variety of defense strategies to resist herbivores, which require transcriptional reprogramming of cells and profound changes in plant metabolism. Due to the large number of genes involved in defense processes, rapid screening strategies are essential for elu ...

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Probability, Statistics, and Computational Science

In this chapter, we review basic concepts from probability theory and computational statistics that are fundamental to evolutionary genomics. We provide a very basic introduction to statistical modeling and discuss general principles, including maximum likelihood and Bayes ...

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The Essentials of Computational Molecular Evolution

In this chapter, we give a brief yet self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present r ...

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Detecting Laterally Transferred Genes

Methods for identifying alien genes in genomes fall into two general classes. Phylogenetic methods examine the distribution of a gene’s homologues among genomes to find those with relationships not consistent with vertical inheritance. These approaches include identifying or ...

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Gene Prediction

Evolutionary genomics is a field that relies heavily upon comparing genomes, that is, the full complement of genes of one species with another. However, given a genome sequence and little else, as is now often the case, genes must first be found and annotated before downstream analyses can be done. Com ...

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Next-Generation Sequencing Technologies and Fragment Assembly Algorithms

As a classic topic in bioinformatics, the fragment assembly problem has been studied for over two decades. Fragment assembly algorithms take a set of DNA fragments as input, piece them together into a set of aligned overlapping fragments (i.e., contigs), and output a consensus sequence for each of t ...

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