Intracellular battlegrounds: conflict and cooperation between transposable elements

Leonardo, Teresa E.; Nuzhdin, Sergey V.

doi:10.1017/s0016672302009710

Cited by 21 publications

(23 citation statements)

References 37 publications

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“…While it is interesting to see these large changes, transposable elements violate the assumptions of the BD model in a number of ways and it can therefore be seen as a validation of our approach that they are identified as unlikely (see Discussion). Regardless of their lack of agreement with our model, the observation that one TE family has expanded and that one has contracted in S. cerevisiae suggests that there may be competition between these intracellular parasites (Leonardo and Nuzhdin 2002).…”

Section: Identification Of Unusually Evolving Gene Families In Sacchamentioning

confidence: 61%

Estimating the tempo and mode of gene family evolution from comparative genomic data

Hahn¹,

Bie²,

Stajich³

et al. 2005

Genome Res.

286

343

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Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.

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Section: Identification Of Unusually Evolving Gene Families In Sacchamentioning

confidence: 61%

Estimating the tempo and mode of gene family evolution from comparative genomic data

Hahn¹,

Bie²,

Stajich³

et al. 2005

Genome Res.

286

343

View full text Add to dashboard Cite

show abstract

“…It has been recently suggested that the relationships between genome components (including genes, transposable elements, or any sequence able to persist over evolutionary time) were similar to the relationships between individuals or species in ecosystems (10,49,50), although the possibility to apply ecological formalism to genome evolution remains questionable (51). Here, we brought substantial evidence that the relationships between autonomous and nonautonomous mariner TE copies were analogous to parasitism: Mos1 copies (the "hosts") are able to survive and replicate by themselves, whereas peach copies (the "parasites") are unable to transpose without Mos1 copies.…”

Section: Discussionmentioning

confidence: 99%

Experimental evolution reveals hyperparasitic interactions among transposable elements

Robillard

Rouzic

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs' activity, interactions, and accumulation dynamics is thus of major interest to understand genome evolution. Here, we describe the transposition dynamics of cut-and-paste mariner elements during experimental (short-and longer-term) evolution in Drosophila melanogaster. Flies with autonomous and nonautonomous mariner copies were introduced in populations containing no active mariner, and TE accumulation was tracked by quantitative PCR for up to 100 generations. Our results demonstrate that (i) active mariner elements are highly invasive and characterized by an elevated transposition rate, confirming their capacity to spread in populations, as predicted by the "selfish-DNA" mechanism; (ii) nonautonomous copies act as parasites of autonomous mariner elements by hijacking the transposition machinery produced by active mariner, which can be considered as a case of hyperparasitism; (iii) this behavior resulted in a failure of active copies to amplify which systematically drove the whole family to extinction in less than 100 generations. This study nicely illustrates how the presence of transposition-competitive variants can deeply impair TE dynamics and gives clues to the extraordinary diversity of TE evolutionary histories observed in genomes.transposable elements | hyperparasitism | Drosophila | experimental evolution | invasion dynamics

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“…Canonical transposable elements, usually considered as parasitic sequences (Doolittle and Sapienza 1980;Orgel and Crick 1980) in the genome of an organism, play the role of the victim when they are in competition with mobile but nonautonomous elements. The complexity of TE evolution thus appears to be partly due to such a multilevel parasitism (Leonardo and Nuzhdin 2002).…”

Section: Discussionmentioning

confidence: 99%

“…What are the similarities between our TE dynamics models and existing predator-prey or host-parasite models? In other words, is this likeness relevant only to a vague, but convenient analogy, or is it an indication of a wide theoretical overlap between, on the one hand, the well-studied and still developing area of interspecific interactions, and, on the other hand, the embryonic theory of genomic ecology (Bascompte and Rodriguez-Trelles 1998;Leonardo and Nuzhdin 2002;Brookfield 2005)? There are indeed striking correspondences between our simple dynamics equations and the basic Lokta-Volterra prey-predator model (Lokta 1925;Volterra 1926).…”

Section: Discussionmentioning

confidence: 99%

Population Genetics Models of Competition Between Transposable Element Subfamilies

Rouzic

Capy

2006

Genetics

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Transposable elements are one of the major components of genomes. Some copies are fully efficient; i.e., they are able to produce the proteins needed for their own transposition, and they can move and duplicate into the genome. Other copies are mutated. They may have lost their moving ability, their coding capacity, or both, thus becoming pseudogenes slowly eliminated from the genome through deletions and natural selection. Little is known about the dynamics of such mutant elements, particularly concerning their interactions with autonomous copies. To get a better understanding of the transposable elements' evolution after their initial invasion, we have designed a population genetics model of transposable elements dynamics including mutants or nonfunctional sequences. We have particularly focused on the case where these sequences are nonautonomous elements, known to be able to use the transposition machinery produced by the autonomous ones. The results show that such copies generally prevent the system from achieving a stable transposition-selection equilibrium and that nonautonomous elements can invade the system at the expense of autonomous ones. The resulting dynamics are mainly cyclic, which highlights the similarities existing between genomic selfish DNA sequences and host-parasite systems.

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Intracellular battlegrounds: conflict and cooperation between transposable elements

Cited by 21 publications

References 37 publications

Estimating the tempo and mode of gene family evolution from comparative genomic data

Estimating the tempo and mode of gene family evolution from comparative genomic data

Experimental evolution reveals hyperparasitic interactions among transposable elements

Population Genetics Models of Competition Between Transposable Element Subfamilies

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