Peer review of: Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium (2020)



  

Reviewers' comments: 

Reviewer #2 (Remarks to the Author): 

The authors successfully addressed my primary concerns and comments. This paper will serve not 
only as an important paper for the polyploid community, but also for the broader genomics community 
as the focus has been shifting towards the importance of analyzing pangenomes. 

Reviewer #4 (Remarks to the Author): 

Gordon et al., Gradual polyploid genome evolution .... 

Thanks for the response on my previous comments and thanks for the exhaustive work on 
restructuring the ms and rewriting large portions of the ms. I really appreciate this. I reread through 
the ms.. It now reads much better than the initial versions, the introduction is much more focussed 
and the discussion got a very impressing overhaul. Nevertheless I still have some points I would like 
to raise: 
line 116: not all of our crops are outbreeders as suggested in this sentence. Think of cereals 
line 138: what are comparative grde genome assemblies?. Unclear 
line 145: post-polyploidisation gene loss is still in its infancy (after 1.4 My). Hmm, some cereal studies 
suggest that this is a very rapid process. Only few generations. Is the basic hypothesis wrong? Does 
out- vs. inbreeding behaviour have impact? Btw: any knowledge about subgenome recombination in 
Brachypodium hybridum? This might have impact on some of the aspects you analyse later on... 
line 180: what are comparative assemblies? 
line 320: referenvce to suppl figure 9a. Should be 9b (?). However in the figure legend it gives 8b... 
Please fix 
line 332: refe to suppl figure 9b. Should be 9c (8c?) 
line 341: Has a reverese cross been done? So swapping of female and male parent. 
line 366 ff: I'm not sure I get the message here. Can you simplify? 
line 372 ff: Selection analysis. The thresholds used are sort of non-traditional thresholds. More 
important the conclusion basically is that no evidence for selection has been found. The whole section 
could be removed or moved into supplement. 
line 424 ff: "extremly subtle bis" is an interesting wording. Basically there is no difference. Please 
shorten this section to aminimum 
line 503: 7 to 2-1 Ma... ???? There is prob atypo but I cannot really decipher what this is supposed to 
tell me 

Figures: In general The quality of the figures is disputable and not always illustrates the point made in 
an appropriate manner: 
why is class 3 missing from figure 6? 
figure 7 asks for some art work. So does fig 4 a and fig 5. There is tendency for info overload in the 
figures... (I'm well aware about the huge amount of data that was used for this work. Nevertheless, 
sometimes a story is better be told by less info-dense figures. 

Again thanks and congratulations for the insightful work! 

Reviewer #5 (Remarks to the Author): 

This is the revised version of a manuscript that I have reviewed a while ago. After a careful reading of 
the new version, I acknowledge that the authors did a good job of revision, and have addressed all of 
the major concerns raised by previous reviewer #3. I have no additional questions.