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

Abstract

In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes. A tripartite TE classification scheme is proposed to account for their replicative, integrative, and structural components, and the need to expand in vitro and in vivo studies of their structural and biological properties is emphasized. Bioinformatic studies have now become front and center of novel TE discovery, and experimental pursuits of these discoveries hold great promise for both basic and applied science.

Keywords: Classification; Mobile genetic elements; Phylogeny; Reverse transcriptase; Transposase.

Fig. 1

The diversity of reverse transcriptases and DDE transposases found in mobile genetic elements. Groups having representatives with solved 3-D structure are underlined. a Phylogenetic analysis of known RTase types (after [88]). In addition to TEs, host genes (TERT, RVT) and non-mobile bacterial RTs are included into the analysis. Also shown are the types of endonucleases/phosphotransferases associated with each RT type. b Dendrogram representation of 19 DDE TPase eukaryotic superfamilies from Repbase (www.girinst.org) and 21 prokaryotic DDE families from ISfinder (www-is.biotoul.fr) databases [29, 133] as of this writing. Left, prokaryotic; right, eukaryotic; middle, with cross-domain representation. The dendrogram is star-like, except for cross-domain families with prokaryotic and eukaryotic branches [71, 74, 75]. Bacterial families are in blue/green; eukaryotic in orange/red/purple. Dotted lines denote clades A, B, C from [76]; smaller clades are not shown; assignment of many TEs to known families could not be performed due to the dearth of known representatives. MuA from phage Mu was assigned to clade A, although it is not represented in ISfinder. The more distantly related RuvC-like DEDD TPases of the RNase H family are not included; neither are the mechanistically different HUH, S, Y, or HEN families

Fig. 2

Graphical representation of the replicative, integrative, and structural components contributing to TE diversity. a Diversity of polymerase-phosphotransferase combinations in mobile elements. The main types of polymerases and endonucleases are in boldface, and are also shown in single-letter codes along the two respective axes. Two-letter combinations are shown for each TE type at the intersections. b Same, with addition of structural components in the third dimension. c A 2-D grid listing the currently known combinations of polymerases and endonucleases. A few additional types of endonucleases found only in group I introns are not shown for simplicity