PONE-D-22-01656Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)PLOS ONE

Dear Dr. Shi,

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PLOS ONE

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Yunnan Province (2018HB086)."

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Overall, the manuscript is well written and data/findings are clearly presented. The methods can be expanded and I have made notes on the manuscript to direct the authors on where to enhance the methods. Likewise, I have provided suggestions for additional literature that can be included in the manuscript at the discretion of the authors.

Reviewer #2: The authors presented a study on three mitogenomes from Macadamia species, and did the comparison of genomic features, repeat sequences, RNA editing, transfer from plastome into mitogenome and phylogeny with other higher plants. This manuscript provides some interesting findings. But there are still a few questions that need to be clarified and improved. In order to make the manuscript much clearer and the conclusions more valid, comments as follows:

1. The Figure 1 on the circular map of three Macadamia mitogenomes, the authors should remake these maps, clear labels for each gene.

2. I suggest the authors take care of the space and consistence on the number and word, for example, “31841bp (cox2)”, there is no space between “31841” and “bp”, but in other places there is space between them; also for the number, “31841” using “31,841” style, etc.

3. The other big problem is the references, the author must be very careful on every reference, such as uppercase, lowercase, italic, journal names, etc. The author must follow the instructions of the reference of this journal.

4. What are the structural differences among the three mitogenomes? How the author verify the accuracy of the three assemblies, especially for a couple of bps difference among these genomes?

5. In the part of “Up to 34.3% (236 sites) RNA editing sites occurred in the first base position of the codon, 68.6% (472 sites) appeared in the second base position, and there was no RNA editing in the third base position.”, why the total percentage > 100%?

6. For the Phylogenetic analysis, the authors need to provide more interesting information or findings.

7. I suggest the authors add more findings from the structural and evolution innovations from these mitogenomes, such as group I and II introns, etc.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-22-01656_reviewer_#.pdf

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

PONE-D-22-01656R1

Dear Dr. Shi,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Please fix the minor issues that the reviewer identified.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Yanbin Yin

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I am pleased with the author's revision and attention to my comments. However, I have two very minor corrections for the authors to address:

Line 56: "Additionally,, they..."

Please remove the redundant comma.

Line 113 -114 : "...and NCBI were used to annotate the mt genome."

Please cite the program also; I apologize that my previous comment was vague regarding an NCBI citation. Did you use ORF finder? If so, please cite: “…and ORF finder (NCBI) were used to annotate the mt genome.”

Reviewer #2: There are minor errors in the manuscript:

1. Line 56, two comma after "Additionally";

2. Line 123, "Macadamia" is not italic.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No