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This volume details the most up-to-date technologies used in plant transposable element studies and provides easy-to-follow protocols. Chapters guide readers on available database resources, annotation of different families of transposon, and experimental methods to detect their transposition intermediates, neo-transposed DNAs, and transposition events. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Plant Transposable Elements: Methods and Protocols aims to provide web-lab and dry-lab methodologies targeted at various levels from beginner to experienced.
List of contents
A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants.- In silico Identification of Stress Associated Transposable Elements in Arabidopsis thaliana using Public Transcriptome Data.- A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants.- A Tutorial of EDTA: Extensive de-novo TE Annotator.- Mining of Miniature Transposable Elements in Brassica species at BrassicaTED.- Genome-wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing.- Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq.- Identification of Active Transposable Elements in Plants: The mobilome-seq Approach.- High-throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.- Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq.- Determination of TE insertion Positions using Transposon Display.- Detection of Transposition Events from Next-Generation Sequencing Data.- Rapid Detection of Transposon-Induced Genome Rearrangements.- Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture.- Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data.- Quantitative Measurement of Transposon Copy Number using the Droplet Digital PCRDetecting Signatures of TE Polymorphisms in Short-read Sequencing Data.- How to Activate Heat-responsible Retrotransposon ONSEN in Brassicaceae Species.- Measurement of Genetic Mobility Using a Transposon-Based Marker System In Sorghum.- Sequence-specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays.- Analysis of Plant DNA Methylation Profiles using R.- Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Seed Tissue Genomic DNA.- Transposon-Based Tagging in Silico using FastPCR Software.- Bamboo Transposon Research: Current Status and Perspectives.
