Like small operons and thus harbour at least two genes. FurthermoreLike small operons and thus

May 18, 2018

Like small operons and thus harbour at least two genes. Furthermore
Like small operons and thus harbour at least two genes. Furthermore, most SINEs or mRNAderived retrocopies are not true genes but inactive pseudogenes (SINEs with extremely high copy numbers). Authors’ response: Of course, we wanted to refer to non-TE sequences. This sentence was changed into “… from other genomic components”. 5) The sentence ” the core of Darwin’s theory was never really questioned” needs qualification. Perhaps, the authors mean that it was never questioned in the scientific community. Even that would be inaccurate, see refs. [9-12]. Authors’ response: This sentence was indeed misleading, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27107493 we meant that it was never successfully challenged. This was fixed in the revision. 6) There are earlier references (in addition to refs. [34,35] concerning “TE as major actors of diversity” [13-15]. Authors’ response: The Kidwell and Lisch (1997) reference seems well adapted here since they review the effects of all classes of TEs in both animals and plants. The second reference illustrates through several examples the involvement of epigenetics in TE-induced phenotypic variations. 7) “homologues of the three proteins involved in RNAi (ARG family, DICER and RdRP) can be found in all supergroups” What is meant by “supergroups” major clades perhaps? Authors’ response: Eukaryotes are divided in 6 clades called supergroups (Rhizaria, Chromalveolates, Archaeplastidae, Opisthokonts. Amoebozoa and Excavates. The very same term is used in the cited reference, and elsewhere to refer to these 6 clades. 8) When discussing the CRISPR elements, it should be mentioned that the small RNAs were acquired from invaders, such as phages. The acquisition of these elements even resembles something akin to Lamarckism [16].Hua-Van et al. Biology Direct 2011, 6:19 http://www.biology-direct.com/content/6/1/Page 21 ofAuthors’ response: We gave a little more details on these very interesting CRISPR elements. Contrary to Koonin and Wolf 2009, we are however a bit reluctant to qualify this process as “Lamarckism” (Lamarck’s theory, which was a general framework to explain evolution, cannot be validated by rare MG-132 site observations in which Darwinian evolution has led to a system superficially similar to Lamarck’s wrong model of evolutionary change). 9) “First they [TEs] can bring sequences in regulating, coding or intronic regions. Those sequences may trigger useful functional changes (expression pattern, alternative splicing, transcription initiation and termination), by the presence of particular motifs or their physico-chemical properties [see [144] as a recent example]. Second, they can bring coding sequences, which modify the initial sequence and create new genes. Concerning “coding sequences” I do not see much difference between “first” and “second”, once you bring TEs into coding sequences, they usually have to be coding or they would destroy the ORF. Authors’ response: Indeed, the second point was already included in the first, and has been removed. 10) “The full domestication is the most extreme case in which the totality of the coding region is used to ensure the new function.” True, but one should find smaller contributions of fragments of TE-derived genes (this is mentioned only in the legend to Figure 2). For example as novel (alternative) exons oder contributing new termini to existing proteins, just as mRNA-derived retrocopies do [17]. Authors’ response: This is what we meant by “extreme case”. We refer to the less extreme cases two paragraphs later, “I.