PONE-D-19-32560

Genome-wide identification and expression analysis of the phosphatase 2A family in rubber tree (Hevea brasiliensis)

PLOS ONE

Dear Dr. Chao,

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 all points raised during the review process, in particular toning down the conclusion that “moderately down-regulated expression of HbPP2As is crucial for the enhanced natural rubber biosynthesis in rubber trees”, as downregulation of PP2As at this point just correlates with enhanced rubber biosynthesis. To underscore a causal relationship, additional experiments are needed. In addition, qPCR data should be made available.

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Veerle Janssens, Ph.D.

Academic Editor

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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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This manuscript shows an analysis of the PP2A subunits in the rubber tree. The experimental part is mainly use of bioinformatics, but also some gene expression analysis is included. The identified subunits are compared with Arabidopsis data and other species for phylogenetic analysis and gene structures. The promoter regions of PP2A genes were analyzed and gave some interesting putative bindings sites for hormone and stress responses.

This is a well written manuscript with some interesting results.

Figure 6. For B55 Subfamily the gene names appear to be missing.

Reviewer #2: The publication describes the identification of Protein Phosphatase 2A family in rubber tree Hevea brasiliensis. Various bioinformatics tools have been applied to investigate the evolutionary background, gene structure, promoter cis-elements and transcriptional activity of the different PP2A subunits. In addition to the bioinformatics analysis, the authors present qPCR data of the transcriptional activity of the PP2A subunits in virgin trees, in tapped trees and in tapped trees after ethrel treatment. The analysis and experiments have been described with appropriate detail and are of good technical quality.

The discussion offers interesting conclusions about the role of protein phosphorylation in the regulation of rubber biosynthesis. The authors bring up that increased protein phosphorylation and transcriptional upregulation of several protein kinases are have been observed after tapping and ethrel application. The manuscript provides evidence that this is coincided with decreased abundance of PP2A transcripts. However, based on the evidence presented in the manuscript, I feel that the main conclusion “moderately down-regulated expression of HbPP2As is crucial for the enhanced natural rubber biosynthesis in rubber trees” is not fully justified. The study does not provide experimental evidence, that the moderate down regulation of PP2As is necessary for the enhanced rubber biosynthesis. Altogether, the manuscript presents interesting findings and new data about PP2As in Hevea brasiliensis but the authors should rephrase the conclusions of the manuscript.

Other comments:

The labeling in the Figure 6 is misleading as the trees were treated with ethrel and not with ethylene.

Although the manuscript is written in good English, I feel that careful editing of the language would enhance the readability of the manuscript.

According to PlosOne policy, the qPCR data presented in the manuscript should be made available for the reader.

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Reviewer #1: No

Reviewer #2: No

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Genome-wide identification and expression analysis of the phosphatase 2A family in rubber tree (Hevea brasiliensis)

PONE-D-19-32560R1

Dear Dr. Chao,

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.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Veerle Janssens, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The authors have adequately addressed the reviewers' and editor's comments

Reviewers' comments: