Umfang:
Online-Ressource (XII, 330 p. 44 illus., 28 illus. in color, digital)
ISBN:
9783642318429
Serie:
Topics in Current Genetics 24
Inhalt:
Transposable elements are DNA sequences with the capacity to move within a genome. Although their presence and impact has long been known, the recent genome-wide analysis of many eukaryotic genomes has uncovered their major role in genome dynamics and function. The present book explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies based on new-generation sequencing. Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail and 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 transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data!
Anmerkung:
Description based upon print version of record
,
Plant Transposable Elements; Impact on Genome Structure and Function; Series description; Preface; Contents; Chapter 1: So Many Repeats and So Little Time: How to Classify Transposable Elements; 1.1 Introduction; 1.1.1 Early Findings on Genome Sizes and Sequence Complexity; 1.1.2 Definition of ``Gene Space´´ and the ``C-Value Paradox´´; 1.1.3 The Number of Genes is Similar in All Genomes; 1.1.4 The C-Value Paradox; 1.2 Transposable Elements; 1.2.1 Basics of Selfishness and Junk; 1.2.2 TE Taxonomy and Classification; 1.2.3 Class and Subclass: The Highest Levels of TE Classification
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1.2.4 TE Superfamilies Represent Ancient Evolutionary Lineages1.2.5 TEs Show Most Diversity at the Family Level; 1.2.6 The 80-80-80 Rule Revisited; 1.2.7 Biological Meaning vs. Pragmatism in TE Classification; 1.2.8 How Many Different TE Families Are There?; 1.2.9 The Necessity of TE Databases; References; Chapter 2: Transposable Element Annotation in Completely Sequenced Eukaryote Genomes; 2.1 Introduction; 2.2 De Novo Detection of Transposable Elements; 2.2.1 Computing Highly-Repeated Words; 2.2.2 All-by-All Alignment and Clustering of Interspersed Repeats; 2.2.3 Features-Based Methods
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2.2.4 Evidence for TE Mobility2.3 Classification and Curation of Transposable Element Sequences; 2.3.1 Classification; 2.3.2 Identification of Families; 2.4 Annotation of Transposable Element Copies; 2.4.1 Detecting TE Fragments; 2.4.2 Filtering Satellites; 2.4.3 Connecting TE Fragments to Recover TE Copies; 2.5 Discussion; References; Chapter 3: Using Nextgen Sequencing to Investigate Genome Size Variation and Transposable Element Content; 3.1 Introduction; 3.2 Exploring the Repetitive Fraction Within and Among Species Using NGS: An Example from the Genus Zea
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3.2.1 Genome Size Variation in the Genus Zea3.2.2 Assessing the Contribution of TE Families to Genome Size Variation Between Maize and Z. luxurians Using NGS; 3.3 Evolution of TE Profiles Through Evolutionary Times: A Comparison Between Zea and Arabidopsis; 3.4 Using NGS to Estimate TE Content and Diversity in Non-model Species; 3.5 Conclusion; References; Chapter 4: Genome-Wide Analysis of Transposition Using Next Generation Sequencing Technologies; 4.1 Introduction; 4.2 Genomic Approaches for the Study of Transposition
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4.3 Use of Next Generation Sequencing Technologies to Study Transposition4.4 Technical Discussion; 4.5 Conclusion; References; Chapter 5: Hitching a Ride: Nonautonomous Retrotransposons and Parasitism as a Lifestyle; 5.1 Retrotransposons; 5.1.1 Retrotransposons, Drivers of Genome Evolution; 5.1.2 Replication of Autonomous Retrotransposons; 5.2 Nonautonomous Transposable Elements; 5.2.1 Nonautonomous Retrotransposons; 5.2.2 Types of Nonautonomous Retrotransposons; 5.2.3 Examples of Type 2 Nonautonomous Retrotransposons; 5.2.4 Examples of Type 3 Nonautonomous Retrotransposons
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5.2.5 Classification of Nonautonomous Retrotransposons
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So many repeats and so little time - How to classify transposable elements -- Transposable element annotation in completely sequenced eukaryote genomes -- Using nextgen sequencing data to investigate genome size variation and transposable element content -- Genome-wide analysis of transposition using Next Generation .-Sequencing technologies -- Hitching a ride: Non-autonomous retrotransposons and parasitism as a lifestyle -- Plant endogenous retroviruses? A case of mysterious ORFsMITEs, miniature elements with a major role in plant genome evolution -- Glue for jumping elements: Epigenetic means for controlling transposable elements in plants -- Responses of transposable elements to polyploidy -- Noise or symphony: comparative evolutionary analysis of sugarcane transposable elements with other grasses -- Helitron proliferation and gene-fragment capture -- Transposable Element exaptation in plants -- SINE exaptation as cellular regulators occurred numerous times during eukaryote evolution -- LTR retrotransposons as Controlling Elements of genome function -- Rider transposon insertion and phenotypic change in tomato -- Retrotransposons and the eternal leaves.
Weitere Ausg.:
ISBN 9783642318412
Weitere Ausg.:
Buchausg. u.d.T. Plant transposable elements Berlin : Springer, 2012 ISBN 9783642437595
Weitere Ausg.:
ISBN 9783642318412
Weitere Ausg.:
ISBN 364231841X
Sprache:
Englisch
Fachgebiete:
Biologie
Schlagwort(e):
Pflanzen
;
Transponierbares Element
;
Aufsatzsammlung
DOI:
10.1007/978-3-642-31842-9
URL:
Volltext
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