The Mitochondrial Genome of Nematodontous Moss Polytrichum commune and Analysis of Intergenic Repeats Distribution Among Bryophyta

Round 1

Reviewer 1 Report

The authors present a well-crafted topic. Stylistically, the manuscript is written clearly and comprehensibly. The results are original and will be a valuable contribution to molecular biological knowledge in mosses. I fully recommend publishing.

Author Response

We are very grateful to the reviewers for a positive assessment of our article and  are very hopeful that now the article can be accepted.

Reviewer 2 Report

I think that the manuscript entitled 'The Mitochondrial Genome of the Nematodontous Moss Polytrichum commune and the uneven Distribution of Intergenic Repetitive Elements Among Bryophyte Lineages' is of great interest.

Some comments and suggestions follow. In my opinion, the English language and style should be revised by a native speaker. I include some comments on expressions that sounded especially strange to me, but I'm not a native speaker myself. There are also some formal aspects that should be amended according to the journal rules.

• Line 1: I think that the manuscript title could be improved. I would recommend to include a verb (Analysis?).
• Line 18: italics are needed for Polytrichum commune
• Lines 23-24: The statement 'According to the 23 whole genome pairwise similarity data Tetraphis pellucida and Buxbaumia aphylla sufficiently differ 24 from other Bryophyta species' needs some further explanation to be put into context.
• Line 25: check expression: 'The first known Bryophyta mitogenome rearrangement was...'
• Line 37: homogenize: ca or ca.
• Line 37: A comma is not needed after species
• line 42: homogenize: a comma should be use to separate thousands, as it is done in the rest of the manuscript
• Line 44: 's' is needed in forms
• Line 44: it is not needed to use 'the' before Polytrichopsida
• Line 45: check expression: considered as 'an' apparently with strikingly analogous 'position' to that of the conifers...
• Line 46: check expression: in terms of 'the' peristome
• Line 48: Polytrichopsida belongS to 'the' nematodontous...
• Line 53: Check spelling: Polytrichopsida
• Line 74: I would recommend to change the expression to 'far from complete'
• Line 77: Notice that higher plants refer to vascular plants, not to bryophytes. Check the intended meaning and correct.
• Line 106 and below: author of plant names should be used whenever the species are first mentioned
• Line 110: genome boundaries WERE
• Line 126: check expression: "Nested repeats all the subunits of which were contained within the subunits of another larger", please amend
• Line 140: the authors indicate that they used GTRGAMMA model, Why did you select this model? Did you run any model selecting program? Please, specify
• Line 147: P. commune here should be not in italics
• Line 152: avoid saying that P. inflexum is the third Polytrichopsida representative if the second representative is not indicated
• Line 167: distribution is misspelling
• Lines 171-173: I would recommend to illustrate the indicated differences in a table or graph
• Line 176: mosses is misspelling
• Line 177: check punctuation (and. Among)
• Page 6, Figure 2: I would recommend to improve these graphs. Use letters to indicate the three parts of the figure, unify the format and size of letters, etc.
• Line 184: comma not needed (one, presented)
• Line 189: the and dot not needed (in Pogonatum inflexum (Figure 3))
• Lines 197-199: Is this part of the Figure 3 legend? If so, please, put it in the appropriate place. Otherwise, move above, to the part of the text where Figure 3 is mentioned
• Lines 213-217: check and amend English expression
• Line 219, Figure 5 legend: the is not needed before Heatmap
• Line 229: based on THE analysis
• Line 231: A closing parenthesis is not needed ([10]. Study) 
• Line 240: indicate number: Table 1
• Page 10, Table 1: I would recommend to include the revised species names in this table. In addition, I find it a little bit complex to search for data, How is this table ordered? I would recommend to reorder the data in a more clear and friendly way.
• Lines 250-252: This is not discussion and should be moved to results section.
• Line 253: Due to THE high
• Line 256: (Figure 5), four groups are well distinguished: I would recommend to indicate the name of the groups within the figure
• Line 262: check punctuation: 99.87%). All
• Line 265: similarity of the whole genomes correspondS
• Line 266: check punctuation, comma not needed: two exceptions explained
• Line 270: those --> these
• Line 271: that is no needed: Remarkably, T. pellucida possesses
• Line 272: check expression: but differs from
• Line 275: check expression and spelling: with other Polytrichopsida
• Lines 278-279: I would recommend to clarify this expression. The authors should indicate that this statement refers to the similarity analysis, but that the phylogenetic tree points to a closer relationship of Buxbaumia with other arthrodontous mosses than with Tetraphis.
• Line 286: Despite the inversion
• Line 287: analysis shows a high
• Line 289: check expression: genomes undergo extensive and high frequent recombination that results
• Line 297: In mosses
• Line 297: indicate number: Table 1
• Line 315: check the expression: Therefore, the inversion observed in the polytrichopsid moss Pogonatum inflexum that is flanked by short 17 bp...
• Lines 328-323: Notice that according to the results presented, species with repeats in intergenic spacers are located in the basal part of the phylogenetic reconstruction, whereas, the most derived groups of mosses lack such repeats. This is the opposite situation than the one stated in this paragraph. The authors should address this and clarify the first sentence of this paragraph, according to the following paragraph.

Author Response

We are very grateful to the reviewers for a positive assessment of our article and especially reviewer 2 for a thorough analysis of the text. We have taken into account all the comments made and are very hopeful that now the article can be accepted.

The detailed response to comments is in the attachment.

Author Response File: Author Response.docx