Plant Transposable Elements

This second editions provide new and updated methods on 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, Second Edition aims to provide web-lab and dry-lab methodologies targeted at various levels from beginner to experienced.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt

A predictive approach to infer the activity and natural variation of retrotransposon families in plants.- Genome-wide identification of miniature inverted-repeat transposable elements by targeted high-throughput sequencing.- eccFinder2: a software dedicated to extrachromosomal circular DNA detection from Nanopore sequencing data, for plant to human samples.- Identification of linear DNA intermediates of long terminal repeat retrotransposons using ALE-seq.- Analysis of sequencing data generated by ALE-seq.- Detection and identification of insertion positions of a mobilized transposable element using Transposon Display.- Detection of transposition events from next-generation sequencing data.- Scalable exploration of complex mobilome activity with high-throughput transposable elements sequence capture in Arabidopsis.- Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data.- Rapid and quantitative assessment of DNA copy number using Droplet Digital PCR.- How to activate heat-responsible retrotransposon ONSEN .- Visualization of somatic retrotransposition in plants using the SAKE reporter system.- A short-read-based approach for detecting transposable element insertions and associated structural variations in rice populations.- ParasiTE: a bioinformatics pipeline to identify chimeric gene-transposon transcripts and associated alternative RNA isoform production.- nanoALE-seq: long-read profiling of active LTR retrotransposons via linear extrachromosomal DNA.- Efficient and quantitative measurement of extrachromosomal DNA using Droplet Digital PCR.- Enrichment of cytoplasmic RNA granules from Arabidopsis for molecular analyses.- Profiling poly(A) tail lengths of transposable element transcripts using Nanopore direct RNA sequencing.- Profiling m6A modification on retrotransposon transcripts by MeRIP-seq.- Analysis of plant DNA methylation profiles using R.- Bamboo transposon research: current status and perspectives.- Systematic identification of de novo somatic and heritable transposition events using deNOVOEnrich.