Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding
, Andrea Silverj 1,2,3, Riccardo Piccinno 1,3,6, Julien Devilliers 7, Clifton Lewis 7, Daniele Arnoldi 3, Fabrizio Montarsi 8, Paula Escuer 9,10, Giuseppe Fusco 4, Veronica De Sanctis 2, Roberto Feuda 7, Alejandro Sánchez-Gracia 9,10, Annapaola Rizzoli 3 and Omar Rota-Stabelli 1,2,3,*Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript by Zadra et al provides a phylogenetic and barcoding studies for Ae. japonicus and Ae. koreicus to clarify the evolution. The authors use a genome skimming approach, a short read and shallow genome sequencing, to determine the divergence time, based on whole mitogenomes.
The study results provide a good primer for a more detailed genome analysis to further characterise the evolutionary lineage of these mosquito species. More interestingly the results show that the estimates of Aedini evolution are more recent than previously reported. The comparison with previously published data is also a good strategy to provide further confidence in the results.
Overall, the manuscript is of high quality and will increase the knowledge of these mosquito species and in future their role in pathogen transmission.
Author Response
>Thanks for your time in reviewing the manuscript.
Reviewer 2 Report
Comments and Suggestions for AuthorsZadra et al. present a very worthwhile contribution to our understanding of the genomics of mosquitoes. I have very few suggestions other than on the written manuscript which are on the scan of the text attached.
One thing though, is I don't see "Genome Skimming" as a separate analytical process from the shallow sequencing which you use, rather it is descriptive of the primary data which was collected i.e. shallow sequencing without any enrichment method such as RAD-seq. Most use of the term in the literature matches this definition (ie of sequencing approach, not analysis) and indeed the figure in Dodsworth which you cite, seems to depict it in this way.
Very minor point, and the rest is quite easy to fix in editing.
Comments for author File: 
Comments.pdf
A number of editorial suggestions to improve the written expression are included in the marked up copy of the manuscript attached.
Author Response
I have very few suggestions other than on the written manuscript which are on the scan of the text attached.
>Thanks for appreciating our work and for the many editorial suggestions that helped improve the English.
One thing though, is I don't see "Genome Skimming" as a separate analytical process from the shallow sequencing which you use, rather it is descriptive of the primary data which was collected i.e. shallow sequencing without any enrichment method such as RAD-seq. Most use of the term in the literature matches this definition (ie of sequencing approach, not analysis) and indeed the figure in Dodsworth which you cite, seems to depict it in this way.
>We agree with the reviewer and amended text to avoid confusion. We deleted “These data allowed us” and “a procedure that” at line 108. We further changed the title and used “Shallow whole genome sequencing” instead of “genome-skimming”. We also deleted “genome-skimming” from the abstract.
A number of editorial suggestions to improve the written expression are included in the marked up copy of the manuscript attached. peer-review-33179490.v1.pdf
> Thanks again for the main editorial suggestion that greatly improved the English of the manuscript.
>Overall we accepted almost all the 221 small edits you have suggested. On many occasions we deleted repetitions and unnecessary adjectives.
>We further edited the Simple Summary to make it clearer.
>Other explicit questions found in the reviewer’s pdf file:
Was any QC performed?
>Yes, but according to Masurca developers, we did not trim the data for the genome assembly. We trimmed for microbial profiling. We added a sentence to clarify this issue.
Line 182: Availability? Please add to supplementary materials.
>We checked our pipeline and found that the concatenation was done using FASconCAT, which we have also used for the mitogenomic dataset. This info has been added.
