title: A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.
abstract: 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).
authors: UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France.
authors: Benoît
authors: B
authors: Piégu
authors: UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France; Institute of Biotechnology, University of Lausanne, Center for Biotechnology UNIL-EPFL, 1015 Lausanne, Switzerland.
authors: Solenne
authors: S
authors: Bire
authors: UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France; Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, United States. Electronic address: parensburger@csupomona.edu.
authors: Peter
authors: P
authors: Arensburger
authors: UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, 37380 Nouzilly, France. Electronic address: yves.bigot@tours.inra.fr.
authors: Yves
authors: Y
authors: Bigot
mesh_terms: D001483:Base Sequence; D002965:Classification; D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D047668:Inteins; D007438:Introns; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D009626:Terminology as Topic
chemical_list: D004251:DNA Transposable Elements; D018626:Retroelements
keywords: Host range; Mobility; Nuclease; Recombinase; Ribozyme; Transposon