PONE-D-20-32528

Transcriptome survey and expression  analysis  reveals effects and metabolic pathways of 'Yulu Xiang' Pear in response to long-term drought stress

PLOS ONE

Dear Dr. Guo,

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Xiang Jia Min, 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: Partly

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 article “Transcriptome survey and expression analysis reveals effects and metabolic pathways of 'Yulu Xiang' Pear in response to long-term drought stress” measures some physiological indicator and has a RNA-Seq on the drought stress pears. I have some suggestions as follows.

1. Combine figure1-figure5 into one figure.

2. Please present the useful information of RNA-Seq in the main text.

3. In Table 2, deferentially is differentially.

4. How many repetitions of the RNA-Seq and other data.

5. Please describe a model in the end of the text based on your data.

6. The results are simple, rewrite it.

Reviewer #2: Though Transcriptome sequencing-based works are very common nowadays for investigating the role, metabolic pathways, the discovery of candidate genes and markers; the manuscript entitled “Transcriptome survey and expression analysis reveals effects and metabolic pathways of 'Yulu Xiang' Pear in response to long-term drought stress” is important by different aspects, one the Pear crop is economically important as its fruits have high demands worldwide and another is the drought stress which causes the serious problems in its production. In the current work, many metabolic pathways are depicted from the transcriptome sequence of the Yulu Xiang Pear, which have major importance in the abiotic stress tolerance in the plant. I appreciate the efforts of the authors and would like to add comments on this research work for some clarity on the following points.

• The authors had mention the water stress condition created for the 12 months by withholding irrigation in the drought stress group, however, there is no evidence shown in the result to monitored the stress level for this large period. They could have to monitor the relative water content, chlorophyll content, cell membrane stability periodically.

• The authors have mentioned the soil relative water content in Pear trees cultivation was achieved 80% and 30% in control and drought stress groups respectively, but it is not cleared that at what stage the said moisture levels were achieved and for how much period these levels were maintained to induce the stress in pear trees.

• The sources for the software packages and databases used for sequence analysis and annotation were not mentioned in the manuscript. The sources/links should be cited or acknowledged in the manuscript.

• The functions of the selected genes for the quantitative real-time PCR analysis were not discussed in the manuscript, on what basis the gene was selected for validation? The candidate genes for drought stress in Pear plant should be discussed in the discussion part of the manuscript correlating with the antioxidant enzymes assay, fruit soluble solids, and photosynthetic characters performed in the current research work.

• Proline content is expected to be increase during drought stress conditions but in the current study, it is lower in drought stress than the control group. Please clarify it in the discussion with reference as it is a contrasting result.

• The antioxidant enzymes SOD, CAT, POD activities reported decreased under drought stress as compared to the control group. At initial stress, these antioxidant enzyme levels should increase but might be because of the long-term moisture stress condition these enzyme activities are reduced. Please give references for the same. Also, the authors why not monitored the enzyme activity during stress conditions periodically so that the stage at which the activity is at its pick level could have detected.

• The changes in fruit soluble solid content and quality of fruit were checked in the current work, have there any impact of drought stress on fruit-bearing and yield were not mentioned, the yield and production-related data of the control and drought stress groups should be included in the results as it directly indicates the stress impact on the production/yield from that plant.

• The discussion part of the manuscript has to improve by including some additional references.

Besides these points, there are some minor typo and grammatical errors are there which need to be corrected.

L 172 – Add “and” in-between two values as it creating the confusions.

L 174 - L 176- Modify the sentence for more clarity.

L 210 - Is the author wants to say “for further study to invest ‘investigate’ the functions of drought stress-responsive genes”? Correct the sentence.

L 231 – L 232- Reference is missing for the statement.

L 258 - L 260- Add reference for the sentence.

Fig. 6 & Fig. 7- The labels of the X-axis are difficult to read, use good quality graphical image.

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Reviewer #1: No

Reviewer #2: Yes: Dr. Pranjali Atul Gedam

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Transcriptome survey and expression analysis reveals the adaptive mechanism of 'Yulu Xiang' Pear in response to long-term drought stress

PONE-D-20-32528R1

Dear Dr. Guo,

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,

Xiang Jia Min, 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: Partly

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: Drought has seriously affected crop production, but the regulatory network of crop stress resistance is not clear,

There is no systematic theory to guide breeding. This paper give some useful informaton. My questions was all addressed, i have no more suggestions.

Reviewer #2: All comments have been address by authors. I want to suggest the authors, the experiment should be designed prior to start the experimental activities, So the observations will not missed on specific stage, which is very important in fruit trees. As the spel of experiment is very long, and it is hard to repeat the experimental activities.

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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: Yes: Dr. Pranjali Atul Gedam