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).

The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

“…Recently, we proposed that this definition needs to be broadened to "TEs are discrete segments of DNA capable of moving within a host genome from one chromosome or plasmid location to another, or between hosts by using parasitic vectors that they use for lateral transfers." 3 An important aspect of this definition is that it includes mobile DNA sequences that are primarily maintained by vertical transmission as copies integrated into the chromosomes or plasmids of their hosts. Therefore, according to this definition, while viruses, phages, and integrative conjugative elements (ICE) have similar features to TEs, they are not considered to be TEs because they are able to move between hosts independently of transmission vectors.…”

“…Based on out findings we concluded that 1) the basal dichotomy view of the TE world advocated by Finnegan is no longer justified by modern science, 2) the Curcio and Derbyshire view appears to us to fit the current science best, but requires careful attention to evolutionary convergences at the molecular level, and 3) the addition of several new TE classes and orders are necessary to keep up with recent discoveries in this field. 3 In Table 1 we outline our proposal for a new taxonomic scheme which has the advantage of allowing the integrating new classes, new orders and new-families, such as the recently described Casposons. 26,27 However, using the same standards as we have applied to previous taxonomic proposal we recognize that our scheme is deficient in several respects.…”

“…The criteria used are indicated in italics just below the levels of Class, Order and Superfamilies. Bibliographic references of updated points with respect to the previous version 3 are indicated. Late in the preparation of this manuscript, on October 19 th 2016, it was reported 34 that two Introner-like elements occurring respectively in the genomes of two unicellular algae, the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferensare, are not TEs with a non-LTR retrotransposon phenotype, but are MITEs related each to a species of DDE-transposons for which the families remain to be identified.…”

“…Recent publications (see discussions in refs. 3,4 ) reflect these views and it is time for the TE community to reexamine the bases upon which its science is organized. We call for the emergence of an international society for the biology of TEs to address these questions by including all the voices in the community, it is time for the "Lion and Rat.…”

A naturalists guide to mobile genetic elements

“…Such community efforts of standardization should also take into account suggestions for a revised classification system, one which better incorporates the diversity of archaeal, bacterial and eukaryotic forms of mobile genetic elements, and based more upon the divergent phylogenetic lineages of these elements (Piégu et al 2015).…”