Mitogenomic Analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the Evolution of the Gene Rearrangements
Round 1
Reviewer 1 Report
Letter to Authors
fishes-2630070-v1
Mitogenomic analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the evolution of the gene rearrangements
Yu Zhang, Lu Qi, Fengping Li, Yi Yang, Zhifeng Gu, Chunsheng Liu, Qi Li, Aimin Wang
230920
Dear authors,
I am sorry to say your MS is a typical horse-deer research where something found in a horse is studied in a deer. One of two mitochondrial genomes sequenced (Pinctada margaritifera) has already been determined and published (HM467838). Mitochondrial gene order rearrangements have already been discussed based on comparative phylogenetic analysis just like yours. Even if you like to publish this mediocre MS with less originality, at least a round of thorough revision is necessary mainly regarding to make it compact. A horse-deer research can be published as a short paper (communication in this journal) with, say, five to six pages long.
I commented some minor points for improvement, but note that it would not at all enough, even if you take all of the following comments into account for revision. Thorough revision and re-organization is definitely necessary.
L11
The mitogenomic evolution of the Pterioidea is still poorly known. -> delete
It is well-known at a level of your analysis.
L14-21
The ATP8 gene .. were inferred -> revise
Mention only what is new.
L28 introduction
Make this section as short as one or two paragraphs with <500 words.
L42-46
For example, .. in the mitogenome of Grapsoidea. -> delete
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research.
L54
only six
Not true. Sequences from Pinctada fusca and P. margaritifera are present.
L64 M&M
Make as short as one or two paragraphs (<500 words) citing some appropriate text book-like papers such as "method X followed a previous report [ref]" or "method Y was employed". Sub-section headers are not necessary.
L111 table 1
Can be put as a supplement.
L112 table 1 body
ANadara broughtonii -> Anadara broughtonii
NC026081,etc
Entries with "NC_" are not the original. See the COMMENT field.
L130 results and discussion
Make as short as two or three paragraphs (<1000 words). General description of the mitochondrial genomes can be omitted. Only specific points should be mentioned. The top paragraph of the sub-section 3.1, sub-sections 3.4 and 3.5 can be retained, but substantial compacting is necessary. Tables 2-6 should be put in supplements or omitted. Figures 2-4 should be omitted or put in supplements. Sub-section headers are not necessary.
L281 conclusion
Make as short as two to three sentences in a veni-vidi-vici style (<100 words).
L302 references
Check the reference list carefully again from the beginning. Reference lists are frequently hotbeds of errors. You might add, omit or swap citation in the main text on the way internal revision. Numbering of the references might then shift. If so, readers think you are making irrelevant citation. It is the authors' responsibility that all references are properly cited.
Check thoroughly to make sure:
if reference numbers are properly presented (L303,etc),
if paper titles are in lower case (L303,etc),
if scientific names are in Italics (L319,etc),
if journal titles are abbreviated when possible (L307,etc),
if abbreviated journal title words accompany a dot (L303,etc),
if journal volume and page ranges are properly scripted (L339,etc),
etc.
See the citation guide at:
https://www.mdpi.com/authors/references/
The following items may be helpful for further analysis and discussion.
Li F, Zhang Y, Zhong T, Heng X, Ao T, Gu Z, Wang A, Liu C, Yang Y. 2023. The complete mitochondrial genomes of two rock scallops (Bivalvia: Spondylidae) indicate extensive gene rearrangements and adaptive evolution compared with Pectinidae. Intl J Mol Sci 24:13844.
Liu F, Li Y, Liu J, Zhang Y, Bao Z, Wang S. 2019. The complete mitochondrial genome and phylogenetic analysis of Spondylus violaceus. Mitochondrial DNA B Resour 4:2908-2909.
Zhan X, Zhang S, Gu Z, Wang A. 2018. Complete mitochondrial genomes of two pearl oyster species (Bivalvia: Pteriomorphia) reveal novel gene arrangements. J Shellfish Res 37:1039-1050.
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references.
Do not make simple repetition of your results in the discussion section. Put then-what matters forward. Use noun phrases to make abstract your results.
Author Response
Dear Reviewer,
First, we would like to say thank you for the comments provided for our manuscript. Those comments are all valuable and helpful for improving our manuscript. We have studied the comments carefully and made corrections in this manuscript. The responses are shown below.
Point 1: L11 The mitogenomic evolution of the Pterioidea is still poorly known. -> delete
It is well-known at a level of your analysis.
Response 1: We have deleted this sentence in response to your comments.
Point 2: L14-21 The ATP8 gene .. were inferred -> revise
Mention only what is new.
Response 2: In this paragraph, we describe the characteristics of the two mitogenomes sequenced in this study and the results of our phylogenetic analysis. These results are based on new data from our research.
Point 3: L28 introduction
Make this section as short as one or two paragraphs with <500 words.
Response 3: We have made changes to the introduction part.
Point 4: L42-46 For example, .. in the mitogenome of Grapsoidea. -> delete
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research.
Response 4: Thank you very much for your suggestion, we have deleted this sentence.
Point 5: L54 only six
Not true. Sequences from Pinctada fusca and P. margaritifera are present.
Response 5: Thank you very much for your correction. We have checked the NCBI database again. Indeed, as you said, P. margaritifera has already been sequenced by others. We are very sorry that we ignored this point before the study in this paper, but our research on P. margaritifera is based on the data of samples collected by ourselves. There is no complete data on the mitogenome of Pinctada fusca in NCBI, only part of the protein coding gene sequence, which can be checked on NCBI. We have corrected the number in the article to 7.
Point 6: L64 M&M
Make as short as one or two paragraphs (<500 words) citing some appropriate text book-like papers such as "method X followed a previous report [ref]" or "method Y was employed". Sub-section headers are not necessary.
Response 6: Thank you very much for your suggestions, which are very helpful to our article. The part of materials and methods we wrote is more helpful for readers to understand the details of our research. As described in other references, we believe that the detailed description of materials and methods is helpful for readers to read this article.
Point 7: L111 table 1
Can be put as a supplement.
Response 7: We have changed this table into table S1 according to your request.
Point 8: L112 table 1 body
ANadara broughtonii -> Anadara broughtonii
NC026081,etc
Entries with "NC_" are not the original. See the COMMENT field.
Response 8: We have modified the Genbank number in the table.
Point 9: L130 results and discussion
Make as short as two or three paragraphs (<1000 words). General description of the mitochondrial genomes can be omitted. Only specific points should be mentioned. The top paragraph of the sub-section 3.1, sub-sections 3.4 and 3.5 can be retained, but substantial compacting is necessary. Tables 2-6 should be put in supplements or omitted. Figures 2-4 should be omitted or put in supplements. Sub-section headers are not necessary.
Response 9: Thank you for your suggestions, which are very helpful to our article. We have revised the contents of the results and discussion section. However, the content of this section is the most important part of the whole article, so we think it is necessary to keep the sub-section headers, as in the other references.
Point 10: L281 conclusion
Make as short as two to three sentences in a veni-vidi-vici style (<100 words).
Response 10: We have modified this part.
Point 11: L302 references
Check the reference list carefully again from the beginning. Reference lists are frequently hotbeds of errors. You might add, omit or swap citation in the main text on the way internal revision. Numbering of the references might then shift. If so, readers think you are making irrelevant citation. It is the authors' responsibility that all references are properly cited.
Response 11: We have carefully read the format requirements of the references and revised our article reference list.
Comments on the quality of English language
Do not make a simple reference list (A stated this, B analyzed that, C argued it, or alike). Simple reference lists bloat your MS, dilute your originality, and undersell your own research. Use noun phrases to make abstract contents of those references.
And do not make simple repetition of your results in the discussion section. Put then-what matters forward. Use noun phrases to make abstract your results.
Response：Thanks for the comments on English quality. We tried to polish the language ourselves, and also polished the language using the MDPI English Editing Service to improve the quality of English.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The manuscript reports the sequences of the mitochondrial DNA of two species of pearl oysters (Superfamily Pterioidea). Various sequence composition statistics are calculated from these sequences. Genes are identified and their order examined, for comparison with previously published data on other species in the order Pteriomorphia to determine what changes have occurred in the evolution of the group. The phylogeny of the group is investigated using mitochondrial rRNAs and protein coding genes.
The methodlogy and analyses are standard for such investigations. However, there are a number of areas where the manuscript could be improved.
(1) More effort to find missing tRNAs in P. albina (trnL and the trnS copies). At the very least BLAST and/or FASTA3 searches should be made of the complete P. albino genome using the sequences of homologue tRNAs.
(2) The discussion in lines 223–251 is rather uncritical. More attention should be given to why there are differences between phylogenies recovered in the various analyses. Is there any reason why the short nuclear data alignment in [77} should be given equal weight with studies based on larger datasets? Why the phylogeny found in the present manuscript, which is based only on mitochondrial genes be more accurate than other studies?
(1) I have some comments on formatting. The lettering in Figure 1 is too small. Perhaps the mitogenomes could be enlarged by showing one above the other instead of side-by-side. It would be more informative if the circles were drawn to scale – then the sizes of the intergenomic regions could be appreciated.
(2) Figure 3 and Tables 5 and 6 report the same data. Why should these be shows in both forms (to me the tables are much more detailed and more informative.
(3) In Figure 5, the font is too small. There is so much space between taxon names that they could be easily enlarged without increasing the overall size of the figure.
(4) According to the instructions to authors, sentence case should be used for journal articles in the list of references, rather than the title case which is now used.
Minor comments:
Line 119: Was convergence checked (e.g. by Tracer) or was 25% a random choice for discarding initial trees.
Line 150: It seems very odd that the 3’ end of Cox 2 should also code for four tRNAa. If this is correct it is worthy of a general comment. Has such a situation been seen in any other species?
Comments for author File: Comments.pdf
Considerable improvement in English usage required. I have made some suggestions on the PDF, especially in relation to usage in the specialist field of evolutionary mitogenomics but the manuscript should also be thoroughly checked by a general English editor. In the text, the definite article (“the”) is commonly incorrectly added to proper nouns (e.g. “the P. albina”). The form “the P. albino mitogenome” is informal (for “the mitogenome of P. albina”) but “the” can be used in this context. Other general issues are the agreement of verb and subject number (i.e. singular or plural), the consistency of tense use (past and present) in the Results,
Author Response
Thank you very much for your suggested changes to this article. We sincerely admire your professionalism. Those comments are all valuable and helpful for improving our manuscript. We have studied the comments carefully and made corrections in this manuscript. The responses are shown below.
Point 1: More effort to find missing tRNAs in P. albina (trnL and the trnS copies). At the very least BLAST and/or FASTA3 searches should be made of the complete P. albino genome using the sequences of homologue tRNAs.
Response 1: Thank you for your advice. We followed your suggestion to find missing tRNA genes in P. albina. The homologue tRNAs were searched by Geneious, but the missing tRNAs still could not be found. We used MITOS, ARWEN, and BLAST to solve this problem, but the results were not satisfactory.
Point 2: The discussion in lines 223–251 is rather uncritical. More attention should be given to why there are differences between phylogenies recovered in the various analyses. Is there any reason why the short nuclear data alignment in [77]should be given equal weight with studies based on larger datasets? Why the phylogeny found in the present manuscript, which is based only on mitochondrial genes be more accurate than other studies?
Response 2: The differences between the phylogenetic trees constructed in the analyses of the references are due to differences in the molecular markers used to perform the phylogenetic analyses, the number of species used to construct the phylogenetic trees, and the species taxa. Although reference 77 chose short nuclear fragments for its molecular markers, the species taxa studied in this article spanned a much larger range, and therefore this study was chosen to be compared with ours. I have revised this point in the article to supplement the explanation. The phylogenetic tree constructed in this study based on the mitochondrial genome received an extremely high level of support and the view that complete mitogenome plays a greater role in phylogenetic studies than nuclear genome has been confirmed by many references, so it can be shown to be more accurate than other studies.
Point 3: The lettering in Figure 1 is too small. Perhaps the mitogenomes could be enlarged by showing one above the other instead of side-by-side. It would be more informative if the circles were drawn to scale – then the sizes of the intergenomic regions could be appreciated.
Response 3: We have adjusted the picture according to your suggestion and enlarged the font size. Circles are drawn to scale, and a description drawn to scale has been added to the picture description.
Point 4: Figure 3 and Tables 5 and 6 report the same data. Why should these be shows in both forms (to me the tables are much more detailed and more informative.
Response 4: We have modified Figure 3 to supplement Figure S1
Point 5: In Figure 5, the font is too small. There is so much space between taxon names that they could be easily enlarged without increasing the overall size of the figure.
Response 5: We have adjusted the font size in Figure 5.
Point 6: According to the instructions to authors, sentence case should be used for journal articles in the list of references, rather than the title case which is now used.
Response 6：We have carefully revised our article reference list.
Point 7: Line 119: Was convergence checked (e.g. by Tracer) or was 25% a random choice for discarding initial trees.
Response 7：Our study was based on the test results of Tracer, which showed that the ess of all parameters was greater than 200, so 25% was discarded.
Point 8: Line 150: It seems very odd that the 3’ end of Cox 2 should also code for four tRNAa. If this is correct it is worthy of a general comment. Has such a situation been seen in any other species?
Response 8：As you say, this phenomenon is quite specific, but it occurs in other species as well, with the following references：
Zhan, X., Zhang, S., Gu, Z., & Wang, A. (2018). Complete Mitochondrial Genomes of Two Pearl Oyster Species (Bivalvia: Pteriomorphia) Reveal Novel Gene Arrangements. Journal of Shellfish Research, 37(5), 1039–1050.
Xiao, S., Wu, X., Li, L., & Yu, Z. (2015). Complete mitochondrial genome of the Olympia oyster Ostrea lurida (Bivalvia, Ostreidae). Mitochondrial DNA. Informa Healthcare.
Point 9: Considerable improvement in English usage required. I have made some suggestions on the PDF, especially in relation to usage in the specialist field of evolutionary mitogenomics but the manuscript should also be thoroughly checked by a general English editor. In the text, the definite article (“the”) is commonly incorrectly added to proper nouns (e.g. “the P. albina”). The form “the P. albino mitogenome” is informal (for “the mitogenome of P. albina”) but “the” can be used in this context. Other general issues are the agreement of verb and subject number (i.e. singular or plural), the consistency of tense use (past and present) in the Results,
Response 9：Thank you for the changes you made to my article. They really helped us a lot and we have revised this article throughout the whole manuscript according to your advice. We have benefited a lot from your pointers. We also polished the manuscript using MDPI English editing service.
Author Response File: Author Response.pdf
Reviewer 3 Report
Reviewer's report
Date: 25 September, 2023
Journal: Fishes
Manuscript ID: fishes-2630070
Title: Mitogenomic analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the evolution of the gene rearrangements
Authors: Yu Zhang, Lu Qi, Fengping Li, Yi Yang, Zhifeng Gu, Chunsheng Liu, Qi Li *, Aimin Wang *
The authors have sequenced complete mitochondrial genomes in two Pterioidea species, Pinctada albina and Pinctada margaritifera. They have detected a number of gene rearrangements within superfamily. Using additional mitochondrial genome sequences from GenBank, the authors reconstructed phylogeny of Pterioidea and provided reliable evidence for the phylogenetic relationships within Pteriomorphia.
The manuscript is clear and well written, with no fundamental flaws and weaknesses, and contains new and interesting data that are sound, adequately described and illustrated, and that may provide important cues to scientists interested in thereby support the usage of mitogenome sequencing in oyster phylogeny. Therefore, after amending the manuscript according to the following suggestion, it is suitable for publication in Fishes.
Minor point:
Line 85: Change “invertebrate genetic codes” to “invertebrate genetic code”.
Page 3, Table 1: The table is not complete. It is important to add the citations for each mitochondrial genome included in this table.
Page 5, Table 2: Insert a space between “Size” and “(bp)”.
Page 5, Table 3: Insert a space between “Size” and “(bp)”.
Page 6, Line 162: Insert a space between “Table” and “4”.
Page 7, Line 173: Insert a space between “and” and “6”.
Page 7, Line 174: Change “Marine” to “marine”.
Page 8, Figure 3, Title: Use Italics for the species names Pinctada albina and Pinctada margaritifera.
Page 8, Table 5: Use a space between the number and parenthesis. For instance, “246.0(1.67)” should be changed to “246.0 (1.67)”. Do the same for all numbers in this table.
Page 9, Table 6: Use a space between the number and parenthesis. For instance, “239.0(1.62)” should be changed to “239.0 (1.62)”. Do the same for all numbers in this table.
Pages 9-10: Lines 192-194: Consider reformulation. The sense is not clear.
Page 10, Line 200: Insert a space between “8285” and “bp”.
Page 12, Figure 5: The numbers on the figure and the species names are very small. Increase the font.
Page 13, Line 260: Correct English “genns”.
Page 13, Figure 6 A: This part is not clear. The pairwise comparison table should be organized in a way to compare first entry with second, third and so on entry. In your table you compare first entry with the same first entry (for instance, Pinctada albina with Pinctada albino). Change or explain better.
Page 14, Legend of the Figure 6, lines 271-272: Consider English revision. The sentence is not clear.
Page 14, Legend of the Figure 6, lines 274: Insert a space between “ C” and “The”.
Pages 16-18. References: The species names must be in Italics.
Lines 192-194: Consider reformulation. The sense is not clear.
"...which may exist in a nucleotide sequence between the second copy of rrnS and Cox1, cause the 193 assembly program cannot map a duplicate reference sequence."
Author Response
Dear reviewer
Thank you for your suggestions. Those comments are all valuable and helpful for improving our manuscript. We have studied the comments carefully and made corrections in this manuscript. The responses are shown below.
Point 1: Line 85: Change “invertebrate genetic codes” to “invertebrate genetic code”.
Response 1：We have revised this spelling error.
Point 2: Page 3, Table 1: The table is not complete. It is important to add the citations for each mitochondrial genome included in this table.
Response 2：We have changed the table into supplementary table S1 and inserted references into the table.
Point 3: Page 5, Table 2: Insert a space between “Size” and “(bp)”.
Response 3：We have corrected the problem.
Point 4: Page 5, Table 3: Insert a space between “Size” and “(bp)”.
Response 4：We have corrected the problem.
Point 5: Page 6, Line 162: Insert a space between “Table” and “4”.
Response 5：We have corrected the problem.
Point 6: Page 7, Line 173: Insert a space between “and” and “6”.
Response 6：We have corrected the problem.
Point 7: Page 7, Line 174: Change “Marine” to “marine”.
Response 7：Thanks to your careful scrutiny and we have revised this spelling error.
Point 8: Page 8, Figure 3, Title: Use Italics for the species names Pinctada albina and Pinctada margaritifera.
Response 8：We have corrected the problem.
Point 9: Page 8, Table 5: Use a space between the number and parenthesis. For instance, “246.0(1.67)” should be changed to “246.0 (1.67)”. Do the same for all numbers in this table.
Response 9: Revised as suggested.
Point 10: Page 9, Table 6: Use a space between the number and parenthesis. For instance, “239.0(1.62)” should be changed to “239.0 (1.62)”. Do the same for all numbers in this table.
Response 10: Revised as suggested.
Point 11: Pages 9-10: Lines 192-194: Consider reformulation. The sense is not clear.
Response 11：We have rephrased this sentence.
Point 12: Page 10, Line 200: Insert a space between “8285” and “bp”.
Response 12：Revised as suggested.
Point 13: Page 12, Figure 5: The numbers on the figure and the species names are very small. Increase the font.
Response 13： We have corrected the problem.
Point 14: Page 13, Line 260: Correct English “genns”.
Response 14：We have corrected the problem.
Point 15: Page 13, Figure 6 A: This part is not clear. The pairwise comparison table should be organized in a way to compare first entry with second, third and so on entry. In your table you compare first entry with the same first entry (for instance, Pinctada albina with Pinctada albino). Change or explain better.
Response 15： Thanks to your careful scrutiny. The numbers in the table represent the similarity of the gene order of the sequences, the larger the number means the more similar the gene order between the two sequences, and the number obtained by comparing the same sequence is the largest, which indicates that the gene order is completely similar. The data were obtained from CREX analysis. The description of the graphs has been modified.
Point 16: Page 14, Legend of the Figure 6, lines 271-272: Consider English revision. The sentence is not clear.
Response 16：We have corrected the problem.
Point 17: Page 14, Legend of the Figure 6, lines 274: Insert a space between “ C” and “The”.
Response 17：Revised as suggested.
Point 18: Pages 16-18. References: The species names must be in Italics.
Response 18：Revised as suggested.
Point 19: Lines 192-194: Consider reformulation. The sense is not clear.
"...which may exist in a nucleotide sequence between the second copy of rrnS and Cox1, cause the 193 assembly program cannot map a duplicate reference sequence."
Response 19：Thanks to your careful scrutiny. We have corrected this sentence.
Thanks again for your careful check of our manuscript. In order to improve the quality of English, we also employed MDPI English Editing Services.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Letter to Authors
fishes-2630070-v2
Mitogenomic analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the evolution of the gene rearrangements
Yu Zhang, Lu Qi, Fengping Li, Yi Yang, Zhifeng Gu, Chunsheng Liu, Qi Li, Aimin Wang
231009
Dear authors,
I am sorry to see this alleged "revised" MS, with nothing improvement but got worth (18 to 19 pages long). A horse-deer research can be published as a short paper (communication in this journal) with, say, five to six pages long.
Reviewer 2 Report
In my opinion, the revision successfully addresses my comments on the original version and has resulted in a well-written, significant article. I have made a few very minor edits for the consideration of the authors on the attached PDF.
Comments for author File: Comments.pdf
