Peer review of: Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian (2020)


 

REVIEWERS' COMMENTS: 

Reviewer #1 (Remarks to the Author): 

I am satisfied with the explanations provided by authors and with the changes they made to the 
manuscript. 
There are few minor modifications/corrections that I leave to the authors to carry out: 

Typo: Camalina stativa → Camelina sativa 

Table 2: “Family” better specify ”Amount of families” 

Table 2, For the SSR line, in columns “Subclass, Superfamily and Family” I would suggest to put “NA” 
(“Not applicable”) since those three features refer to TEs 

It seems to me that the numbering of Supplemental figures is offset by 1: 

line 164: Supplemental figure 2b should be Supplemental Figure 1b 

line 168 Supplemental figure 2a should be Supplemental Figure 1a 

line 178 Supplemental figure 3 should be Supplemental Figure 2 

line 201: supplemental figure 4 should be Supplemental figure 3 

line 214: as line 201 

line 236: Supplemental Figure 5 should be Supplemental Figure 4 

line 269: Supplemental Figure 6 should be Supplemental Figure 5 

and so on, I suspect. Please check. 

Reviewer #2 (Remarks to the Author): 

The authors have done a good job of addressing my concerns. 

I appreciate the comparisons to similarly aged polyploids. It's not crucial, but I wanted to bring up 
that there are cases of similar complete synteny from much older 'diploidized' WGDs. For example, the 
Juglandaceae (e.g. https://www.nature.com/articles/s41438-019-0139-1) ... it appears that this 
polyploidy event is >60My old and synteny is nearly complete. I don't think this voids the idea that 
teff is 'exceptional', but could be brought up in the discussion if the authors felt it appropriate. 

For completeness, I'd like to address some of the comments made in the response to reviews: 

In the response to reviews, you present the presence/absence of homeologous exchange as a 
hypothesis, but in the main text it is presented as a tested result: '... we detected no evidence of 
recent homoeologous exchange' line 264 ... I don't see methods or results related to tests for 
suppressed homeologous exchange. Am I missing something? There are published tests for this using 
shared vs. unique kmers or snps. 

In terms of the pseudogene discovery method outlined in the response to reviews; I see the results, 

but I'd like a more detailed description of the methods in the main text. Like you say, this is an often 
overlooked test. Others will want to follow what was done here. 

Reviewer #4 (Remarks to the Author): 

Hopefully this will be clear in the web interface, but I am not reviewer #3 and was brought in 
specifically to review the points raised by Reviewer #3 and the author's responses to each point. 

Reviewer 3, Point #1: My reading is that this may be a miscommunication to some extent between 
the reviewer and the authors and could be addressed by providing ciations to support the sentences 
on line 50-51 (characteristics of teff), 51-52 (grown primarily by subsistence farmers), 52-53 (number 
of cultivars developed), 53-54 (resilience of teff and tolerance for semi-arid soils) and/or omiting 
sentences from that set for which there are not good citations. 

Point #2: I think the author's response here is fine. The phylogenetic placement of teff relative to 
other species with complete genome sequences is not at all ambiguous, and while studies of the 
placement of each subgenome relatve to other species in the genus Eragrostis might be interesting, in 
order to be novel they would require sequence from large numbers of genes in several of these 
species. 

Point #3: The authors have provided a thoughtful response here about the two possible explanations: 
extinct diploid progenitors and incomplete sampling. Obviously it would never be possible to PROVE 
extinction but I would suggest that they also discuss the potential that this is simply an issue of 
incomplete sampling of related species. This could be as simply as another clause added on to the 
sentence on lines 66-68. 

Point #4: Agreed. Comparing gene numbers between completely different structural annotation 
pipelines is always going to produce different numbers of gene models for technical, rather than 
biological, reasons. 

Point #5: New text does a good job of addressing this concern. 

Point #6: Change in title addresses this concern. 

Point #7: Clarification in the text is good. I agree with the author's point, but as Reviewer #3's 
comment illustrates the reason for the mismatch between LGs and Pseudomolecules may not be 
apparent to many readers who have not previously worked in this area. 

Point #8: Looks good. 

Point #9: Authors have addressed it by removing this phrase.