Plant Transposable Elements

1. Front Matter

   Pages i-xii

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2. So Many Repeats and So Little Time: How to Classify Transposable Elements

   • Thomas Wicker

   Pages 1-15

3. Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

   • Timothée Flutre, Emmanuelle Permal, Hadi Quesneville

   Pages 17-39

4. Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content

   • Concepcion Muñoz-Diez, Clémentine Vitte, Jeffrey Ross-Ibarra, Brandon S. Gaut, Maud I. Tenaillon

   Pages 41-58

5. Genome-Wide Analysis of Transposition Using Next Generation Sequencing Technologies

   • Moaine Elbaidouri, Olivier Panaud

   Pages 59-70

6. Hitching a Ride: Nonautonomous Retrotransposons and Parasitism as a Lifestyle

   • Alan H. Schulman

   Pages 71-88

7. Plant Endogenous Retroviruses? A Case of Mysterious ORFs

   • Howard M. Laten, Garen D. Gaston

   Pages 89-112

8. MITEs, Miniature Elements with a Major Role in Plant Genome Evolution

   • Hélène Guermonprez, Elizabeth Hénaff, Marta Cifuentes, Josep M. Casacuberta

   Pages 113-124

9. Glue for Jumping Elements: Epigenetic Means for Controlling Transposable Elements in Plants

   • Thierry Pélissier, Olivier Mathieu

   Pages 125-145

10. Responses of Transposable Elements to Polyploidy

    • Christian Parisod, Natacha Senerchia

    Pages 147-168

11. Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses

    • Nathalia de Setta, Cushla J. Metcalfe, Guilherme M. Q. Cruz, Edgar A. Ochoa, Marie-Anne Van Sluys

    Pages 169-192

12. Helitron Proliferation and Gene-Fragment Capture

    • Yubin Li, Hugo K. Dooner

    Pages 193-217

13. Transposable Element Exaptation in Plants

    • Douglas R. Hoen, Thomas E. Bureau

    Pages 219-251

14. SINE Exaptation as Cellular Regulators Occurred Numerous Times During Eukaryote Evolution

    • Jean-Marc Deragon

    Pages 253-271

15. LTR Retrotransposons as Controlling Elements of Genome Response to Stress?

    • Quynh Trang Bui, Marie-Angèle Grandbastien

    Pages 273-296

16. Rider Transposon Insertion and Phenotypic Change in Tomato

    • Ning Jiang, Sofia Visa, Shan Wu, Esther van der Knaap

    Pages 297-312

17. Retrotransposons and the Eternal Leaves

    • Antonella Furini

    Pages 313-324

18. Back Matter

    Pages 325-330

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Transposable elements are short lengths of DNA with the capacity to move between different points within a genome. This process can affect the function of genes at or near the insertion site. The present book gives an overview of the impact of transposable elements on plant genomes and explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies like “new generation sequencing.” Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail, and also illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that they are not just “junk DNA.”

• gene function
• plant genome
• transposable elements

From the reviews:

“For the 16 chapters of this volume, the editors have brought together contributors from all corners of the diverse field of transposon biology. … This volume is pitched to both transposon biologists and to nonspecialists. … the book provides a good introduction to this very broad research field and will be a key reference for specialists.” (J. Arvid Ågren, The Quarterly Review of Biology, Vol. 88 (3), September, 2013)

• , Institut Jean-Pierre Bourgin (IJPB), INRA Versailles, Versailles Cedex, France

  Marie-Angèle Grandbastien

• , Centre de Recerca en Agrigenomica (CRAG), CSIC-RTA-UAB, Barcelona, Spain

  Josep M. Casacuberta

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