Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.
Highlights
Transposable elements (TE), frequently called “selfish genes” [1], “selfish DNA” [2], or junk or garbage DNA, according to the categories defined by Graur et al [3], present several genetic characteristics that allow them to rapidly invade genomes and populations, as well as to sometime to settle there permanently
Another possible clue that can be used when enough copies, both within species and/or from more or less closely related ones, is the TE phylogenies. While these phylogenies are generally incongruent with those of the species, it could be interesting to compare the evolution rate of the different copies. Even if in these types of constructs are based on a mixture of dead, non-autonomous, and active copies, an indication of a domestication/exaptation can be provided by the existence of long branches, which are the signatures of rapid evolution
On the one hand, when TE activities are modulated by epigenetic marks, the two entities can benefit from such a situation, if epigenetic regulation persists over several generations, due to their inheritance, as described in Arabidopsis thaliana [170]
Summary
Transposable elements (TE), frequently called “selfish genes” [1], “selfish DNA” [2], or junk or garbage DNA, according to the categories defined by Graur et al [3], present several genetic characteristics that allow them to rapidly invade genomes and populations, as well as to sometime to settle there permanently. Several non-autonomous or dead copies, or even pieces of TE, can be preserved with non-neutral effects on individual fitness, due to their particular insertion site or the acquisition of new characteristics after a more or less lengthy coevolution with genomes During this coevolution process between TE and genomes, various interactions and trajectories can lead to the emergence of relatively stable evolutionary states, usually described as taming, domestication, or exaptation. This tinkering may be due to the shuffling and association of different parts of a genome by ectopic recombination, transposition, gene duplication, frameshift mutation, translocation, or, again, autopolyploidy in plants This dynamic can be fueled by the acquisition of external genetic material, as a result, for example, of interspecific hybridizations or horizontal transfers (HT). Since TEs are entities subject to HT between species—the source of genetic variability and tinkering within the genome—it is interesting to detail their dynamics through the evolutionary “dialogue” between them and their genomic ecosystems, after their arrival in a naïve genome
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