Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes

Abstract

Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II elements present in genomes as high-copy-number populations of small and highly homogeneous elements. While virtually all class II transposon families contain non-autonomous defective transposon copies, only a subset of them have a related MITE family. At present it is not known in which circumstances MITEs are generated instead of typical class II defective transposons. The ability to produce MITEs could be an exclusive characteristic of particular transposases, could be related to a particular structure of certain defective class II elements, or could be the consequence of particular constraints imposed by certain host genomes on transposon populations. We describe here a new family of pogo-like transposons from Medicago truncatula closely related to the Arabidopsis Lemi1 element that we have named MtLemi1. In contrast to the Arabidopsis Lemi1, present as a single-copy element and associated with hundreds of related Emigrant MITEs, MtLemi1 has attained .30 copies and has not generated MITEs. This shows that a particular transposon can adopt completely different strategies to colonize genomes. The comparison of AtLemi1 and MtLemi1 reveals transposase-specific domains and possible regulatory sequences that could be linked to the ability to produce MITEs.

A Divergent P Element and Its Associated MITE, BuT5, Generate Chromosomal Inversions and Are Widespread within the Drosophila repleta Species Group

“…Similar to nonautonomous elements, MITEs transpose using transposases encoded by autonomous elements. A distinctive feature of MITEs is their homogeneity in size and sequence, which differentiates them from typical nonautonomous elements, which are usually unique defective copies (Guermonprez et al 2008). Moreover, some MITEs are not just deletion derivatives of complete transposons and unlike other nonautonomous TEs have internal sequences unrelated to their master copies (Feschotte et al 2003).…”

“…Their high copy numbers, homogeneous size, and high similarity within MITE families distinguish them from the typical defective nonautonomous transposons, which are usually unique copies (Feschotte et al 2002; Guermonprez et al 2008). Although MITEs were discovered in plants (Bureau and Wessler 1992, 1994), they have been found in a variety of organisms, including Drosophila (Smit and Riggs 1996; Tu 2000; Holyoake and Kidwell 2003; de Freitas Ortiz et al 2010).…”

hAT transposable elements and their derivatives: an analysis in the 12 Drosophila genomes

“…However, some exceptions exist; D. yakuba has an intermediate TE content (12.04%) and few hAT derivatives. This variation can be explained by differences in genome colonization strategies, differences in the phases of colonization strategy in the same genome or both (Guermonprez et al 2008). Bonnivard et al (2002) has described the hobo element have a tri-amino acid repeat-motif encoding the amino acids threonine, proline and glutamine (TPE) that is polymorphic among populations of D. melanogaster.…”

MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi

“…Copies of a MITE could vary in sequence length, TIRs and DRs, etc. (Tu, 2001;Guermonprez et al, 2008). So it is difficult to propose whether such predicted MITE candidates are false positives, and manual inspection is needed to investigate this question.…”