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PONE-D-22-01083Characterization of the genome and silk-gland transcriptomes of Darwin’s bark spider (Caerostris darwini)PLOS ONE

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[We thank our many colleagues who kindly shared their expertise, time, resources, and insights over the long history of this project, including J. Retief, and T. Orpin, J. Coddington, John Hogenesch, and members of the Voight Lab (past and present). B.F.V. is grateful for support of the work from the Alfred P. Sloan Foundation (BR2012-087). We thank the MICET crew in Antananarivo, H. Rabarison, S. Rahanitriniaina, and O. Raberahona for their help in the field. Genomic assembly was conducted on the PMACS HPC infrastructure at the University of Pennsylvania, funded in part by NIH Special Instrumentation Grant 1S10OD012312-NIH.]

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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: The manuscript “Characterization of the genome and silk-gland transcriptomes of Darwin’s bark spider (Caerostris darwini)” by P.L. Babb et al. is acceptable for publication in Plos One after minor revision.

The paper presents the whole sequencing of the genome of the Caerostris darwini spider with special attention to the spidroin genes. The same research group performed the first complete sequencing of the genome of a spider (Triconephila clavipes), which led to identification of the full set of spidroin genes in one species. Technically the work is irreproachable and the analysis highlights what the authors consider as the main findings of their work.

Consistently with this judgement, there are just a couple of suggestions with regard to the manuscript before being finally published.

1) Since the authors make an extensive comparison between the spidroin genes of Caerostris darwini and Triconephila clavipes, it would be helpful if they devote a few sentences to explain the phylogenetic relation between both species and their location in the Araenomorphae lineage.

2) The authors mention twice that “C. darwini...whose dragline is the toughest known biomaterial on Earth” (Abstract) and “…to create the toughest silks that have been documented to date [3]”. (Introduction). Undoubtedly, C. darwini spins one of the toughest spider silks, however, other spiders such Argiope aurantia (see Madurga et al., Scientific Reports 6:18991 (2016)) show comparable or even higher values of work to fracture. Therefore, I would recommend to downgrade the previous sentences to “… whose drageline is one of the toughest known biomaterials on Earth” and “…to create one of the toughest silks …”.

3) The authors rise the critical question of gene expression at several points along the manuscript: “These observations motivated further work …as well as their presumably complex expression across morphologically distinct silk glands” (Introduction) and “Previous work has demonstrated that spidroins assigned to a particular gene class are not exclusively transcribed in the silk gland in which the gene is assigned” (Results, Line 282). I fully agree with this view of the Authors and I think it is worth highlighting that similar conclusions are found through the proteomic analysis of protein expression of silk glands in orb-weaving spiders (Jorge et al., J. Exp. Zool. Part B, https://doi.org/10.1002/jez.b.23117).

Reviewer #2: Some minor suggestions:

1. As bulky amount of data was presented, descriptions linking to methods in the main text could be more specific, for example, “……for along with those we previously reported in T. clavipes (Methods)” (line 198), which part of the “Method”?

2. How to approach some of the data in detail? For example, “three C. darwini spidroins – Sp_81.2, SpL_133.2, and SpL_4399.2 – eluded assignment to any of the previously established classes based on sequence homology alone（line 187-188）” , but it’s not very direct to get these sequences and the relevant analysis, which is actually of real interest.

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Reviewer #1: No

Reviewer #2: No

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Characterization of the genome and silk-gland transcriptomes of Darwin’s bark spider (Caerostris darwini)

PONE-D-22-01083R1

Dear Dr. Voight,

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,

Serena Aceto, Ph.D.

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: All comments have been addressed

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

**********

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: The paper is acceptable for publication in its present form. The authors have addressed all my previous concerns.

Reviewer #2: The authors presented genomic dissection of Darwin’s bark spider, Caerostris darwini, and focused on the new putative spidroin genes. The data has been clearly and systematically presented.

This manuscript is therefore suggested for direct acceptance.

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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