A Field Guide to Eukaryotic Transposable Elements

Abstract

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.

Keywords: genome evolution; retrotransposons; transposable element origins; transposition mechanisms; transposons.

Figure 1.. Summary of replication mechanisms and transposition intermediates

Proposed transposition intermediates and key replication steps for five TE subclasses. YR-retrotransposons and Maverick/Polintons are not shown, but the former are expected to transpose via the same intermediate as Class II YR-transposons (i.e. Cryptons). The mechanism of Mavericks/Polintons has not yet been studied, but based on the presence of protein-primed type B DNA polymerase (pPolB), they are expected to transpose by direct synthesis of a DNA copy (78). For comprehensive reviews on transposition mechanisms see (29, 68).

Figure 2.. Structure and taxonomy of eukaryotic TEs

Left panel: unrooted cladograms showing putative relationships between the major TE superfamilies, based on phylogenies of core protein domains for five subclasses (4, 36, 67, 88, 95, 167). Right panel: genetic structures of representative elements from each subclass. Outlined boxes are open-reading frames, shaded regions are defining protein domains, kinked lines are introns, triangles are repeated sequences and rounded boxes (i.e. for Alu) are RNA elements. Domains with the same colours (excepting gray) indicate shared ancestry. Element lengths not to scale.

Figure 3.. Distribution of TEs across the eukaryote phylogeny

Reference genome size (sea green circles) varies dramatically across eukaryotes and is loosely correlated with transposable element content. Here, the honey bee TE content is likely an underestimate, as approximately 3% of the genome derives from unusual “large retrotransposon derivatives” (LARDs) (39). For ease of visualisation, DIRS elements have been included with LTRs and all Class II elements included under “DNA”. Data was acquired from genome RepeatMasker output files. Credit to Matt Crook for Volvox carteri silhouette and to Huang et al. for the figure inspiration (71).