Retrotransposon Sequence Variation in Four Asexual Plant Species

Abstract

Abstract. Transposable elements (TEs) can be viewed as genetic parasites that persist in populations due to their capacity for increase in copy number and the inefficacy of selection against them. A corollary of this hypothesis is that TEs are more likely to spread within sexual populations and be eliminated or inactivated within asexual populations. While previous work with animals has shown that asexual taxa may contain less TE diversity than sexual taxa, comparable work with plants has been lacking. Here we report the results of a study of Ty1/copia, Ty3/ gypsy, and LINE-like retroelement diversity in four asexual plant species. Retroelement-like sequences, with a high degree of conservation both within and between species, were isolated from all four species. The sequences correspond to several previously annotated retroelement subfamilies. They also exhibit a pattern of nucleotide substitution characterized by an excess of synonymous substitutions, suggestive of a history of purifying selection. These findings were compared with retroelement sequence evolution in sexual plant taxa. One likely explanation for the discovery of conserved TE sequences in the genomes of these asexual taxa is simply that asexuality within these taxa evolved relatively recently, such that the loss and breakdown of TEs is not yet detectable through analysis of sequence diversity. This explanation is examined by conducting stochastic simulation of TE evolution and by using published information to infer rough estimates of the ages of asexual taxa.

The Fate of Transposable Elements in Asexual Populations

“…This process of element accumulation is accelerated in smaller populations, with larger initial copy numbers, and with weaker selection. This is consistent with the results for TE sequence evolution in simulations with no excision, where no stable equilibrium in copy number was ever reached (Docking et al 2006). This suggests that asexual populations with no excision of TEs are likely to accumulate large numbers of copies within a time frame of millions of generations, even if the effective population size is in the millions.…”

“…Above this number, a runaway process of element buildup is observed (results not shown). No stable equilibrium with an intermediate TE copy number was ever observed, consistent with results from an asexual model of TE sequence evolution for simulations in which TE inactivation through mutation was not included (Docking et al 2006). We calculated the proportion of simulation runs where TEs were eliminated, to examine the conditions under which asexual populations are expected to cure themselves of deleterious TEs or be driven to early extinction.…”

“…TEs can decay after accumulating mutations, but it seems likely that they will continue to multiply upon the abandonment of sex, given that the rate of inactivating mutations in TEs is probably similar to the rate of transposition (Nuzhdin et al 1998). Docking et al (2006) carried out simulations of TE sequence evolution after the abandonment of sex, including the effects of inactivating mutations, They found that, while all elements were eventually lost from asexual populations, it took many thousands of generations for selection on TE sequences to be relaxed, even with higher mutation and transposition rates than expected in nature. This suggests that new asexual lineages should indeed harbor many active TEs, perhaps for millions of generations assuming a scaling of parameters similar to that done in our model.…”

The Elusive Clone – In Search of Its True Nature and Identity

“…M! stands for mutation risks generations are responsible for the fact that thus far, no putative ancient asexual lineages have been identified in plants (Docking et al 2006; see also Chapter 3). Any models predicting early extinction of clonal lineages through the accumulation of (deleterious) mutations would have to incorporate significantly higher rates in groups with vegetative asexuality, due to the potential incorporation of somatic mutations.…”

Analysis of Rice Genome Long Non-Coding RNA Sequences

“…Majority of repeats that occurred belong to the DNA/TcMarStowaway, RC/Heltron, DNA/PFHarbnger, Simple repeat, DNA/CMCEnSpm and DNA/MULEMuDRclass/family. These repeats mainly constitute class II type transposable elements which move directly by a 'cut and paste' mechanism [23].…”