PONE-D-21-04340

Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

PLOS ONE

Dear Dr. Mascarello,

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PLOS ONE

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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: Partly

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

Reviewer #1: N/A

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Reviewer #1: Yes

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Reviewer #1: 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: This manuscript " Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species" by Prof. Maurizio Mascarello et al., use high-throughput sequencing to obtain the complete de-novo chloroplast genome of 62 commercial African timber species. Then, authors performed a comparative genomic analysis to mine new candidate molecular markers for the discrimination of closely-related tree species. The article is interesting and will be useful in wildlife forensic species identification. Unfortunately, analysis and interpretation of the data in my opinion is not well done. Authors overemphasized the polymorphisms for these timber species, and only compare the variations between related species. For the application of forensic species identification, author should use these cp genome data to develop markers for species identification. I thought that authors should consider to develop the InDel markers, it will be a fast procedure for species identification. After developin, the PCR amplification should be performed for validating the InDel markers in related species.

L109 chloroplast genes revised to chloroplast genome.

L113 in the angiosperms

L186 check the value “160774 bp ± 602”?

L195 Table 1 37.4±0.0, 36±0.0, 36.8±0.0

L274 Millettia, be italic

L455-456 How to know paraphyletic with the genus Hymenaea? No phylogenetic tree

L491 No difference between Khaya grandifoliola and Khaya senegalensis. No indel existed between two species?

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Reviewer #1: No

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Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species

PONE-D-21-04340R1

Dear Dr. Mascarello,

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.

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,

Tzen-Yuh Chiang

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)

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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: (No Response)

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

Reviewer #1: (No Response)

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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: (No Response)

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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: (No Response)

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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: According to the author’s responses, I agreed the point that that SNPs in these highly polymorphic regions provided genetic information for future species identification. Because of low number of gaps (no longer than 1 bp), no relevant InDels were found.

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Reviewer #1: No