Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?

@article{gren2011CoevolutionBT,
  title={Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?},
  author={J. Arvid {\AA}gren and Stephen I. Wright},
  journal={Chromosome Research},
  year={2011},
  volume={19},
  pages={777-786}
}
Most models of genome size evolution emphasize changes in relative rates of and/or the efficacy of selection on insertions and deletions. However, transposable elements (TEs) are a major contributor to genome size evolution, and since they experience their own selective pressures for expansion, genome size changes may in part be driven by the dynamics of co-evolution between TEs and their hosts. Under this perspective, predictions about the conditions that allow for genome expansion may be… 
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TLDR
It is found that variation in sexual/asexual reproduction cannot explain the almost two-fold variation in genome size and using whole genome sequences of three species of varying genome sizes and reproductive system found that genome size was not associated with transposable element abundance; instead the larger genomes had a higher abundance of simple sequence repeats.
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References

SHOWING 1-10 OF 101 REFERENCES
Transposon dynamics and the breeding system
TLDR
A modeling approach was used to investigate how the rate of self-fertilization influences the population dynamics of transposable elements and the strength and effectiveness of selection against transposons was reflected not only in their equilibrium abundance, but also in the per-site element frequency of individual insertions and the coefficient of variation in copy number.
A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?
TLDR
Seed plants do not support the Lynch and Conery mechanism of genome size evolution, and further work is needed to disentangle contrasting effects of mating systems on the efficacy of selection and TE transmission.
The evolution of self-regulated transposition of transposable elements.
TLDR
The conditions under which self-regulated rates of transposition can evolve in populations of transposable elements infecting sexually reproducing hosts are examined to show that both types of regulation can easily evolve in hosts with low rates of genetic recombination per generation.
LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model
TLDR
A review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective, leads to the emergence of a new model for plant genome evolution that takes into account both genome size increases and decreases.
Evolutionary dynamics of transposable elements in a small RNA world.
TLDR
A genome defense system of RNA-mediated silencing also plays a crucial role in limiting TE proliferation and a full understanding of TE evolutionary dynamics must consider how these forces jointly determine their proliferation within genomes.
Insertion-deletion biases and the evolution of genome size.
TLDR
The mutational equilibrium model is found to be problematic, and it is noted that DNA loss by small indels is too slow in real time to determine variation in genome size above a relatively low threshold.
The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata
TLDR
The differences in TE distributions between the two Arabidopsis species represents a synthesis of evolutionary forces that include the transposition dynamics of individual TE families and the demographic histories of populations.
Did Genetic Drift Drive Increases in Genome Complexity?
TLDR
It is concluded that current datasets do not support the hypothesis of a mechanistic connection between Ne and genomic attributes, and it is suggested that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.
Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.
TLDR
A model in which host silencing of TEs near genes has deleterious effects on neighboring gene expression, resulting in the preferential loss of methylated TEs from gene-rich chromosomal regions is presented.
A role for host–parasite interactions in the horizontal transfer of transposons across phyla
TLDR
Evidence that host–parasite interactions have promoted the HT of four transposon families between invertebrates and vertebrates is presented and the large amount of DNA generated by the amplification of the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.
...
1
2
3
4
5
...