Transposable elements and factors influencing their success in eukaryotes

Abstract

Recent advances in genome sequencing have led to a vast accumulation of transposable element data. Consideration of the genome sequencing projects in a phylogenetic context reveals that despite the hundreds of eukaryotic genomes that have been sequenced, a strong bias in sampling exists. There is a general under-representation of unicellular eukaryotes and a dearth of genome projects in many branches of the eukaryotic phylogeny. Among sequenced genomes, great variation in genome size exists, however, little difference in the total number of cellular genes is observed. For many eukaryotes, the remaining genomic space is extremely dynamic and predominantly composed of a menagerie of populations of transposable elements. Given the dynamic nature of the genomic niche filled by transposable elements, it is evident that these elements have played an important role in genome evolution. The contribution of transposable elements to genome architecture and to the advent of genetic novelty is likely to be dependent, at least in part, on the transposition mechanism, diversity, number, and rate of turnover of transposable elements in the genome at any given time. The focus of this review is the discussion of some of the forces that act to shape transposable element diversity within and between genomes.

Figure 1

TEs are broadly classified into 2 classes. Class 1 retrotransposons move using an RNA intermediate, and class 2 the DNA transposons utilize a DNA intermediate. The presence and orientation of repeated DNA structures flanking or within the TEs are indicated by arrows. The black arrows are TIRs. The gray arrows are direct repeats. The striped arrows indicate a repeated sequence or palindrome within the DNA. The gray-hatched boxes indicate the proteins encoded by autonomous TEs, the number of ORFs is so indicated.

Figure 2

The distribution of eukaryotic genome projects mapped in a phylogenetic context. A survey was undertaken of eukaryotic genomes with sequencing projects completed or underway. Both the presence and abundance, of genome sequencing projects in a specific phylogenetic branch is indicated by a gray circle. The size of the circle is meant as a rough indication of total number of projects. The smallest circle indicates a single project and the largest indicating >50 projects. A = supergroup Plantae, B = supergroup Excavate, C = supergroup Rhizaria, D = supergroup Unikonts, E = supergroup Chromalveolates (phylogeny redrawn from Keeling et al. 2005).

Figure 3

Variation of TE composition across genomes. For each species, the relative proportion of RNA and DNA TEs was calculated. The data were compiled either from the corresponding papers reporting draft genome sequences or from the following sources: nematode C. Feschotte, personal communication; rice (Jiang et al. 2004) and N. Jiang, personal communication; Entamoeba (Pritham et al. 2005); Giardia lamblia (Arkhipova and Morrison 2001); Trichomonas vaginalis (Pritham et al. 2007); and Ellen Pritham (unpublished data). The species are Hs = Homo sapiens, Mm = Mus musculus, the nematode, Caenorhabditis elegans, Dm = Drosophila melanogaster, De = Drosophila erecta, Ag = Anopheles gambiae, Aa = Aedes aegypti, Ed = Entamoeba dispar, Eh = E. histolytica, Ei = E. invadens, Em = E. moshkovskii, Sc = Saccharomyces cerevisiae, Sp = Schizosaccharomyces pombe, At = Arabidopsis thaliana, Os = Oryza sativa japonica, Gi = Giardia lamblia, Tv = Trichomonas vaginalis.