A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

Détails

Ressource 1Télécharger: BIB_71563EC2D515.P001.pdf (1822.76 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_71563EC2D515
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Synthèse (review): revue aussi complète que possible des connaissances sur un sujet, rédigée à partir de l'analyse exhaustive des travaux publiés.
Collection
Publications
Titre
A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.
Périodique
Molecular Phylogenetics and Evolution
Auteur(s)
Piégu B., Bire S., Arensburger P., Bigot Y.
ISSN
1095-9513 (Electronic)
ISSN-L
1055-7903
Statut éditorial
Publié
Date de publication
2015
Volume
86
Pages
90-109
Langue
anglais
Résumé
The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).
Mots-clé
Base Sequence, Classification, DNA Transposable Elements/genetics, Evolution, Molecular, Inteins, Introns, Retroelements/genetics, Sequence Analysis, DNA, Terminology as Topic
Pubmed
Web of science
Open Access
Oui
Création de la notice
15/07/2015 10:39
Dernière modification de la notice
20/08/2019 14:29
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