Plant Transposable Elements: Methods and Protocols

ISBN-13: 9781071611364 / Angielski / Miękka / 2022

Cho, Jungnam

Opis

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.

Spis treści

1. A Predictive Approach to Infer the Activity and Natural Variation of Retrotransposon Families in Plants

Matthias Benoit and Hajk-Georg Drost

 

2. In silico Identification of Stress Associated Transposable Elements in Arabidopsis thaliana using Public Transcriptome Data

Doğa Eskier and Gökhan Karakülah

 

3. A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants

Liliane Santana Oliveira, Tharcísio Soares de Amorim, Daniel Longhi Fernandes Pedro, Fábio Fernandes da Rocha Vicente, and Alexandre Rossi Paschoal

 

4. A Tutorial of EDTA: Extensive de-novo TE Annotator

Weijia Su, Shujun Ou, Matthew B. Hufford, and Thomas Peterson

 

5. Mining of Miniature Transposable Elements in Brassica species at BrassicaTED

Murukarthick Jayakodi and Tae-Jin Yang

 

6. Genome-wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing

Yanyan Tang, Fengxia Liu, and Lubin Tan

 

7. Identification of Extrachromosomal Circular Forms of Active Transposable Elements Using Mobilome-Seq

Sophie Lanciano, Panpan Zhang, Christel Llauro, and Marie Mirouze

 

8. Identification of Active Transposable Elements in Plants: The mobilome-seq Approach

Michael Thieme and Anne C. Roulin

 

9. High-throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq

Ling Wang, Eun Yu Kim, and Jungnam Cho

 

10. Bioinformatics Analysis Guides to LTR Retrotransposon-Derived Extrachromosomal Linear DNAs Identified by ALE-seq

Ling Wang, Jungnam Cho, and Viswanathan Satheesh

 

11. Determination of TE insertion Positions using Transposon Display

Eun Yu Kim, Wenwen Fan, and Jungnam Cho

 

12. Detection of Transposition Events from Next-Generation Sequencing Data

Akio Miyao

 

13. Rapid Detection of Transposon-Induced Genome Rearrangements

Sharu Paul Sharma and Thomas Peterson

 

14. Detection of Transposable Element Insertions in Arabidopsis Using Sequence Capture

Leandro Quadrana, Amanda Bortolini Silveira, Erwann Caillieux, and Vincent Colot

 

15. Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data

Baduel P., Quadrana L., and Colot. V.

 

 

16. Quantitative Measurement of Transposon Copy Number using the Droplet Digital PCR

Wenwen Fan and Jungnam Cho

 

17. Detecting Signatures of TE Polymorphisms in Short-read Sequencing Data

Christoph Stritt and Anne C. Roulin

 

18. How to Activate Heat-responsible Retrotransposon ONSEN in Brassicaceae Species

Hidetaka Ito

 

19. Measurement of Genetic Mobility Using a Transposon-Based Marker System In Sorghum

Jae Il Lyu, Yeong Deuk Jo, Joon-Woo Ahn, Jin-Baek Kim, and Soon-Jae Kwon

 

20. Sequence-specific Amplified Polymorphism (SSAP) and Sequence Characterized Amplified Region (SCAR) Markers in Zea mays

Neha Samir Roy, Rahul Vasudeo Ramekar, and Nam-Soo Kim

 

21. Analysis of Plant DNA Methylation Profiles using R

Marco Catoni and Nicolae Radu Zabet

 

22. Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Seed Tissue Genomic DNA

Mayumi Iwasaki and Luis Lopez-Molina

 

23. Transposon-Based Tagging in Silico using FastPCR Software

Ruslan Kalendar, Dana Kospanova, and Alan H. Schulman

 

24. Bamboo Transposon Research: Current Status and Perspectives

Muthusamy Ramakrishnan, Kim Yrjälä, Viswanathan Satheesh, and Mingbing Zhou