Review for "Contrasting genome dynamics between domesticated and wild yeasts"

Completed on 23 Sep 2016 by Casey Bergman . Sourced from http://biorxiv.org/content/early/2016/09/22/076562.

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Comments to author

Author response is in blue.

1) It might be because this is a relatively recent posting, but I couldn't find the 15 Supplemental tables referred to in the manuscript file. Could you please post these supplemental files as part of the preprint subission if you haven't already?

I will post the supplementary tables during the weekend as a revision of this manuscript. I am currently at a conference and the internet is not fast enough for uploading files to bioRxiv -- it got frozen at 76.6% ...

2) The ENA accession for the PacBio data only has 10 strains in PRJEB7245, however 12 are reported in the manuscript. Could you please add the additional 2 PacBio datasets to PRJEB7245?

I think the reads that you saw now is the old reads that we generated using older PacBio chemistry (mentioned in our manuscript). Our collaborators at Sanger Institute have submitted all the new reads for 12 strains to ENA before our submission. But it might take a few days before the newly uploaded reads become public available.

3) The ENA accession for the PacBio data does not appear to provide a mapping between yeast strain names and ENA sample accessions. Could you please post this information as a comment here and correct the sample accession in PRJEB7245 to include strain names?

Thanks for pointing to us this reference. I will check those Ty1 insertions during the weekend and add this reference in our revised manuscript if needed. Actually, in our manuscript, we cited two other references that are even earlier about these Ty1: Wheelan et al. 2006; Shibata et al. 2009.

4) Additional Ty1 insertions on ChrIII that are missing from the S. cerevisiae reference genome have been sequenced and reported previously in Hoang et al (2010): http://journals.plos.org/plosg.... It would be worth comparing your results to theirs and citing their paper for precedence if the new Ty loci are the same.