PONE-D-21-20796

Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.)

PLOS ONE

Dear Dr. Shinozuka,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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ACADEMIC EDITOR: As Peer-reviewers suggest modifications in the manuscript address all their comments critically and resubmit your manuscript.

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Shunmugiah Veluchamy Ramesh, PhD

Academic Editor

PLOS ONE

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Additional Editor Comments:

Reviewers suggest minor revisions to the manuscript. I suggest you to address their comments critically  and resubmit your manuscript for further consideration. Adequate discussion of published research pertaining to horizontal gene transfer is warranted.

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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

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: 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

Reviewer #3: 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

Reviewer #3: 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 authors compared the transcriptome data between bent grass and E. amarillans and identified two horizontally transferred candidate genes. Phylogenetic analysis showed that BGNL was transferred into a common ancestor of Agrostidinae species, while FMOL was transferred into Agrostis stolonifera from Epichloe lineage. The research is structured in an appropriate manner. As there is no functional analysis, the last paragraph "adaptation mechanisms of flowering plants (Angiosperms)" is an over interpretation from the present results. Overall, this manuscript is technically rigorous and meets the scientific and ethical standard, and only minor corrections are needed.

Fig.1a

As Perennial ryegrass is not the main focus of this study, it is better to place it in the third lane.

Furthermore, is there a clear reason why Fig.1a should include the amino acid sequence of perennial ryegrass and Fig.1b should contain the amino acid sequence of E. festucae?

Is there a problem with comparing only E. amarillans and Creeping bent grass?

L241-L244

I could not understand why it is unsuitable for calculating relative gene expression in AsFMOL. Why not just increase the number of cycles?

L269

fine--leaves -> fine-leaves

L307

in cool cool-season grasses -> in cool-season grasses

Reviewer #2: 1. Fungus-originated glucanase and monooxygenase genes in creeping bent grass manuscript is well planned and comprehensive, covering all the aspects of recent studies have revealed presence of fungus-originated genes in genomes of cool-season grasses, suggesting occurrence of multiple ancestral gene transfer events between the two distant lineages. The current article describes identification of glucanase-like and monooxygenase-like genes from creeping bent grass, as lateral gene transfer candidates. The quality of language is good and flow of ideas is easily be followed by the reader. The strength of this manuscript is that discussed almost all the recent research articles related to the research and listed in reference list.

2. The quality of the figures and/or table is satisfactory

3. The manuscript covered the topic in an objective and analytical manner

and reference list covered the relevant literature adequately and in an unbiased manner.

4. I would suggest this manuscript is accepted only after minor corrections are incorporated as suggested below.

Suggested corrections:

In Text:

Some references are not according to the journal format, it has to be modified accordingly.

Reviewer #3: In this research glucanase-like and monooxygenase-like genes were identified as lateral gene transfer candidates in creeping bent grass. In- silico studies were conducted using transcriptome datasets to identify these genes in related plant species. PCR based screening were further performed to confirm the results. In addition gene expression studies were conducted to validate the expressions of these genes. Overall this research provides important information regarding the later genes transfer in creeping bent grass and the scientific quality of the research is high. Following point may be considered.

There are previously published reports regarding the lateral gene transfer in grasses. Authors should discuss in more details regarding the major outcome of this research and highlight its importance.

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Reviewer #1: Yes: Ryo Fujimoto

Reviewer #2: No

Reviewer #3: No

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Fungus-originated glucanase and monooxygenase genes in creeping bent grass (Agrostis stolonifera L.)

PONE-D-21-20796R1

Dear Dr. Shinozuka,

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,

S.V. Ramesh, PhD

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

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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

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

Reviewer #1: 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

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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

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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: The authors responded my comments and I agreed with their comments. Thus I do not have further comments.

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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