Diversity Chromosome Evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH
Round 1
Reviewer 1 Report
In this manuscript, with applying the sequencing, phylogenetic, and cytogenetics analysis, authors found the typical structure, high to 5.12 × 103 copy numbers, and chromosomal distribution of Ty1-copia retrotransposons in Pennisetum purpureum. This research reveals the diversification of Ty1-copia retrotransposons, suggesting differential dynamic evolution directions of Ty1-copia retrotransposons within P. purpureum. Moreover, it has the significance for generation of valid chromosomal markers in retrotransposon families which can be used for its improvement in future. This study was well designed, summarized, and presented here. However, there are still some minor concerns with me in this manuscript.
- Line 87, Why was Fujian elephant grass used in your study? Please note it in your revised manuscript.
- In Figure 4, 6, and 7, I think “the metaphase chromosomes” that you designated are in the prometaphase stage. Please use accurate metaphase chromosome pictures, when all chromosomes condensed extremely and line up at equator.
- Figure 5, the definition is poor. Please replace it with good one.
- How did you identify the chromosomal locations of copia-type retrotransposons? You should detail it in Materials and Methods of your manuscript.
- Line 386, is the format with “science” right? Please also recheck other format errors in reference part of your manuscript.
Author Response
Dear editor and reviewers:
We thank you for your time to process our manuscript “Diversity chromosome evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH”. All comments and suggestions from reviewers are very helpful for revising and improving our manuscript. In this revised version, changes to our manuscript within the document were all highlighted by using red colored text. Point-by-point Responses to the reviewers are listed below this letter.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The manuscript entitled 'Diversity chromosome evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH' is interesting. There is not much information available from forage plants and this manuscript gives some important insights, but, there are multiple issues to be addressed.
General comments
There is no uniformity in writing. For eg. Ty1-copia, written copia in italics and normal in many places. All scientific names are to be italicized.
Specific comments
Line 97-98: It is not mentioned what type of Taq polymerase authors has used for amplification of fragments. It is very important to mention it because all sequencing and downstream sequence analysis depends on PCR amplification and polymerase used.
Line 101: What was the rationale for selecting 88 clones randomly? Why not a round figure like 80 or 100?
Line 107: Any preference for using MEGA 7 instead of recent versions of MEGA?
Line 144, 153, 159, 176, 184, .......: All scientific names must be in italics.
Line 145: Out of these 88 randomly picked clones, none of the clones were repeated with the same size?
Line 150-153: What do you mean by defective? All longer sequences contain all three conserved motifs and with what is mentioned as defective? Also, what do you mean by non-functional? How can you conclude like that? Explain.
Line 151-152: Table S1 is missing.
Line 154: It is not clear how the authors did the nucleotide translation to amino acid. Did they consider all three or six translations or did they start the translation from a forced sequence boundary?
Line 157-158: I am not sure how the authors classified the phylogeny into 28 groups?
Line 163: Figure1: How are these 28 groups classified? I could see many clusters within a clade are considered separate groups. For example, Pc5 and Pc6 in the same cluster are considered different groups. Explain.
Line 164: In Table 1, I could see many N/A. These are unique sequences in the phylogeny
Line 173: What you mean by potentially functional Ty1-copia RT domains?
Line 178: Normally frameshift mutations can lead to stop codons. In this case, it happened or the sequences analyzed contained both?
Line 194: Figure 2, it may be better if you can introduce an outgroup of Ty1-copia sequence and developed the phylogengy. That may give more clarity and a better clustering pattern.
Line 255: ........located in two chromosome 2 (Fig 6). What did you mean by two chromosome 2?
Line 321-322: Need to rewrite for better clarity.
Discussion needs to be modified and rewritten.
Author Response
Dear editor and reviewers:
We thank you for your time to process our manuscript “Diversity chromosome evolution of Ty1-copia Retrotransposons in Pennisetum purpureum Revealed by FISH”. All comments and suggestions from reviewers are very helpful for revising and improving our manuscript. In this revised version, changes to our manuscript within the document were all highlighted by using red colored text. Point-by-point Responses to the reviewers are listed below this letter.
Author Response File: Author Response.pdf
