Novel Perspectives on Chloroplast tRNA Genomic and Structural Variations Imply the Evolution of Papilionoideae (Fabaceae)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

It seems, that this study sampled their 265 taxa on the previous phylogenetic study, since authors referred clade with inverted repeats (IR) and linages without IRs (abstract and lines 72-78 for example). If it is not possible to present/reproduce in this study as a Supplementary File such phylogenetic clade from the published phylogeny, or  at least mention the number of the figure in which such previous clade can be identified.

Well I consider that the resolution and quality of all of the figures must be improved.

I do not like Table 2 the labels are very repeated, however, I do not know how to improve the quality of this table, probably is better to use a figure instead a table for this type of results.  

Lines 277-278: “Most dramatically, the number 18 identified 277 indel”: is unclear, what is number 18?

I suggest that authors emphasize in your discussion or conclusions which are the results that change the perspectives of considering the evolution of either the Papilionoideae or the chloroplast genome.

The supplementary file S1, I suggest that the species of each of the tribes are alphabetically ordered. I recommend that it is necessary to include a column with the source that sequenced such genomes.

I consider that the legend of Table S5 needs more details in order to clarify these results: indicating AC-loop =, ANC-loop=; V-loop=

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The reviewed paper is devoted to the comparison of tRNA genes in plastid genomes of the IRLC members compared with other papilionoid legumes. The authors worked on a representative dataset and applied adequate methods for analysis, so the results obtained are reliable and interesting for the understanding the patterns of genome evolution in this diverse clade. Generally, the paper is written well and reports mostly statistical results without getting deeper into evolutionary interpretations of the findings. Probably some discussion on this matter could be broadened but not necessary.
All my comments and suggestions are available in the manuscript file (see attached) and will not be discussed here in detail. I would suggest that the authors should avoid presenting the same quantitative data in the text and in tables; the latter form is much easier to read. However, large tables and figures (Figure 2, Table 4) are better to be moved to the supplementary materials. At the moment, they are very large and, especially in the case of Figure 2, not that easy to see in present resolution.
The authors should revisit their figures representing quantitative data and statistics, as they lack many important details, such as markers of statistical significance and the explanation of designations.
Some of the pieces of this text need to be rephrased to avoid confusion or make them more comprehensible.
After these changes are made, this paper can be accepted for publication in Horticulturae. In my view, the scope of this paper suits better some journal like Plants, which is devoted to more general aspects of plant science, but it is just a note. 

Comments for author File: Comments.pdf

Comments on the Quality of English Language

The most of the suggestions and corrections made are dealing with style rather than grammar. In several cases, some rephrasing is needed.

Author Response

Thank you for your useful comments and suggestions for our manuscript entitled “Novel perspectives on chloroplast tRNA genomic and structural variations imply the evolution of Papilionoideae (Fabaceae)” (horticulturae-3137030: minor revisions). We really appreciate the comments and suggestions of the editor and the reviewers, and we have revised the manuscript accordingly. All the authors listed have approved the manuscript that is enclosed. I would like to declare on behalf of my co-authors that the work described was original research that has not been published previously, and is not under consideration for publication elsewhere, in whole or in part. We hope that the revised manuscript is now suitable for your journal. Revised portion are marked in “Revised Manuscript with Track Changes”. Thank you very much for your consideration. In case of any questions, please feel free to contact me.

Reviewer 2 has provided comments directly on the PDF version of the manuscript. Therefore, this point-by-point response was also made based on this PDF file, with each response corresponding to the specific comment annotated by the reviewer. When you click on each of the reviewer's annotated comments, our response will appear directly below your comment.

Please see the attachment.

Author Response File: Author Response.pdf