N numerous other cases, the domestication concerns only a part of
N numerous other cases, the domestication concerns only a part of the TE protein […]”. Here, the domain function is exapted. Smaller contributions are mentioned in the next part, which depicts exaptation of TE sequences (and not TE protein function). In some cases, exapted sequences become part of a coding region. 11) “While first examples of TE domestication and cooptation appeared as the exception (although of prime importance in regard to the function), the recent and numerous data prove that this is actually a recurrent phenomenon in genome history. Since the beginning, genomes regularly feed on TEs,” and “TE and genome have been in constant contact since probably the beginning of life and such promiscuity has had repercussions on the evolution on both partners.” Genomes ARE transposed (RNA) elements [5-8,18]. Authors’ response: In this paragraph, we refer to transposable elements, and not to other sequences retroprocessed accidentally. We think that “transposition” is too specific to be applied to any kind of reverse-transcription event.Reviewer’s response: There is not much order PD150606 difference between class I transposable elements (retroposons) and other retroprocessed sequences. Once more, the key to the difference lies in the properties of the RNA: some are more others less efficient templates for retroposition. Where do you draw the line: One hundred retrocopies of a tRNA are retropseudogenes and one thousand copies of a tRNA or tRNA-like RNA are SINEs? Authors’ response: The copy number is clearly not the good criterion to decide whether a sequence is a TE or not. The property to be efficiently retroposed is crucial, and must not depend PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26104484 on the environment, meaning that basically, RNA produced from any intact retroposed copy must keep the ability to be reinserted. 12) page 25, Exploiting TE sequences A discussion about the persistence of exapted TEs in short evolutionary branches (gain and loss of exapted TEs e.g., in primates) [19] and long evolutionary branches (e.g., constitutive expression of exapted TEs in deep mammalian branches) [20] should be added. Authors’ response: This discussion on the long-term persistence of domesticated sequences is indeed interesting, and is now mentioned in the manuscript. However, it is also important to consider that there is no strong evidence that TE-derived exons behave in a different way than new coding sequences from different origins, and that this could simply reflect the “average” fate of genetic novelties in genomes. Reviewer’s response: Agreed, there should be no difference between TE-derived novel exons and those from anonymous genomic sequences [8], because even the latter are ancient TEs who are not discernible anymore, due to mutations over long time periods [6,18]. Actually, most if not all genomic DNA is TE-derived, which would return us to evolutionary transitions following the RNA and RNP-worlds [5,6]. 13) Page 32, TE competition and ecology of the genome For marsupials, Nilsson et al. could show an overlapping activity of RTE and LINE mobilized SINE elements along a single phylogenetic marsupial branch. The parallel activity of the two different retropositional systems was further supported by detecting frequent nested insertions of RTE in LINE mobilized elements and vice versa [21]. Authors’ response: There is indeed no doubt that several TE families can be active simultaneously in genomes. Reciprocal transpositions in inserted copies is a strong piece of evidence that this was.