PONE-D-19-31134

Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after the transition from autotrophic to heterotrophic growth condition in the microalga

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: Yes

Reviewer #2: Partly

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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 entitled “Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after the transition from autotrophic to heterotrophic growth condition in microalga” by Panahi et al., attempted to integrate the weighted gene co-expression network analysis (WGCNA) with transcriptome meta-analysis, connectivity analysis, functional enrichment, and hub genes to uncover the key metabolic targets underpinning the key biochemical pathways in microalgae. Though there are previous studies available in various microalgae including heterotrophic Auxenochlorella protothecoides (PubMed ID: 25012212), Asterarcys sp. (Li et al., 2020, Algal Research, vol. 45, 101753), here the authors used an integrated approach to overcome the existing hurdles. Though the study seems to be interesting, the following comments may be addressed.

1. The methods section is vague. What was the screening condition as mentioned in the data collection? It was stated that authors retrieved dataset PRJNA484804 which contains "3 samples of photoautotrophic cultures" and "9 samples of heterotrophic cultures", which is unclear, specifically about the heterotrophic cultures. Thus, the section may be rewritten.

2, It is not clear whether the authors considered a study network with more different experimental groups to expand the number of independent samples.

3, The authors could compare the current systems biology approach to the previous RNA-seq transcriptomic profiling result to show the highly significant positive correlation over all, also its limitations and strengths.

Minor comments:

1. For photoautotrophic culture, the authors shall mention the dark:light regime for algal cultivation (L. No. 82).

2. Unit for illumination shall be mentioned as μmol photons m−2 s−1 instead of lux (L. No. 83).

3. It is well known that growth phase during the cultivation period varies among the microalgae, thus it is necessary to provide the transition period between log and metabolite accumulation phase (L. No. 87).

Reviewer #2: WGCNA has powerful pontetial to search for genes of interests and even Hub genes for organims adapt to some environmental traits. Very limited studies were done in cyanobacteria and microalgae. Thus this ms had a very intertesting try. With two gene expression datasets, the authors managed to target some hub genes, which difinitely attract interests in the fields of microalgae and environmental sciences to students, researchers and investigators. However, there are several technique concerns about this study. First of all, two sets of data were obtained through different experiments and thus the basis for comparison and integration of these two data would be a questionable issue. The reliablity of the results would be discounted becuase of their different experiment conditions. Another minor issue about the WGCNA results, we nornally could obtained some significant modules, in colors and co0efficient factors with p-values. If have any, please provide and analyze. If not, please also explian.

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Reviewer #1: No

Reviewer #2: Yes: Jiangxin WANG

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Systems Biology Approach Identifies Functional Modules and Regulatory Hubs Related to Secondary Metabolites Accumulation after Transition from Autotrophic to Heterotrophic Growth Condition in Microalgae

PONE-D-19-31134R1

Dear Dr. Panahi,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

O. Roger Anderson

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for promptly attending to your revisions. The reviewers recommend acceptance of your revised manuscript.

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 #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 #2: Yes

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

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 #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 #2: 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 #2: The ms has been improved in the revised version. The concerns in my previous review were solved and added in the main text. I think now it is good to go.

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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.

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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 #2: Yes: Jiangxin WANG