A unified classification system for eukaryotic transposable elements

  title={A unified classification system for eukaryotic transposable elements},
  author={Thomas Wicker and François Sabot and Aur{\'e}lie Hua-Van and Jeffrey L. Bennetzen and Pierre Capy and Boulos Chalhoub and Andrew J. Flavell and Philippe Leroy and Michele Morgante and Olivier Panaud and Etienne Paux and Phillip SanMiguel and Alan H. Schulman},
  journal={Nature Reviews Genetics},
Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the… 

A unified classification system for eukaryotic transposable elements should reflect their phylogeny.

This work proposes the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts.

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

An overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes.

TEsorter: lineage-level classification of transposable elements using conserved protein domains

TEsorter is proposed, which is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs), and its results can also directly reflect phylogenetic relationships and diversities of the classified LTR- RTs.

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To accurately identify, classify, and annotate the TEs in eukaryotic genomes requires combined methods and useful information is provided for biologists who are not familiar with these approaches to find their way through the forest of programs.

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At each step of the TE annotation process, from the identification of TE families to the annotation of TE copies, this chapter outlines the tools and good practices to be used.

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An overview of transposable elements biodiversity is presented, and different approaches to transposability elements detection and analyses are discussed.

Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

Good practice required for manual curation of TE consensus sequences is described and it is suggested that combined approaches, using both de novo and knowledge-based TE detection methods, are likely to produce reasonably comprehensive and sensitive results.

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An overview of transposable elements (TEs) biodiversity and their impact on genomic evolution is presented.



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Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and

Dynamics and evolution of trans-posable elements

This text presents the evolution of transposable elements (TE) and introduces the analysis of the phylogenies of TEs and their interpretations according to different models, for example, horizontal versus vertical transmission.

Classification and nomenclature of retrotransposable elements

  • P. Capy
  • Geology
    Cytogenetic and Genome Research
  • 2005
There is clear evidence of the need to adopt a general and a common classification of retrotransposable elements, and the first classification is now out of date, and must be revisited to take account of the discovery of new elements.

Molecular architecture of a eukaryotic DNA transposase

This work reports the three-dimensional structure of a functionally active form of the transposase from Hermes at 2.1-Å resolution, which has some structural features of prokaryotic transposases, including a domain with a retroviral integrase fold.

Abundance, distribution and dynamics of retrotransposable elements and transposons: similarities and differences

It is shown that the traditional division into two classes, based on the transposition mechanisms, becomes less obvious when other factors are taken into consideration, and a great diversity in distribution and dynamics within each class is observed.

CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements1

It is concluded that CACTA elements contribute significantly to genome size and to organization and evolution of grass genomes.

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All eukaryotic TEs described are found including an extraordinary prevalence of active members of the pogo family, leading to significant advances in perception of the mechanisms underlying genetic changes in these organisms.

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Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs).

A model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements is suggested.

Plant genome organisation and diversity: the year of the junk!