Integration of the Physiology, Transcriptome and Proteome Reveals the Molecular Mechanism of Drought Tolerance in Cupressus gigantea
, Lei Tao 1 and Fanjuan Meng 1,2,*
Round 1
Reviewer 1 Report
The manuscript Integration of the Physiology, Transcriptome and Proteome reveals the molecular mechanism of drought tolerance in Cupressus gigantea presents a comprehensive reseacrh on the response of C. gigantea to drought using physiological, transcriptomic and proteomics techniques.
The manuscript is clear written, understandable and with a few English typos-.
However the results are not new in the sense that similar data have been described in many other plants species, most of all model species such as Arabidopsis. I do not see what is the reason to perform such research, even thoud that C. gigantea is known as quite drought resistant species. Therefore such results are quite expected.
Methods are very low described and more details should be provided, as I suggest in the list below.
Furthermore the raw data ( such spectra and others) from proteomics analysis must be loaded on proteomics data base as PRIDE cPRIDE - Proteomics Identification Database (ebi.ac.uk) as requested by MIAPE (The Minimum Information About a Proteomics Experiment (MIAPE) | HUPO Proteomics Standards Initiative (psidev.info)..
Data can be cripted until publication, but the key for access to the loaded data should be provided to the reviewers to control the experiment.
Line 15: The name of the studied plant Cupressus gigantea should be in italics
Line 347 delete ensuing
Line 348 please add information on the centrifugation after ice cold acetone washing
IAM? Specify the name of the reagent, not only the acronym
Line 334-340 : describe all the protocols used to determine the proline , total sugars, and the activity of the antioxidant enzymes in details.
Line 368: explain what the normalization factor for protein identification was
Line 407 : describe the protocol of total RNA extraction in details
Author Response
Response to Reviewer 1 Comments
Thank you very much for your affirmation of our work and your constructive comments on current manuscript. We have carefully studied the comments on a point-by-point basis and revised our manuscript accordingly. The modifications we made are detailed in our replies below: (The original Reviewers’ comments are colored blue). We hope that you will find the changes and this revised version will be suitable for publication in forests.
Yours sincerely,
Fanjuan Meng PhD,
Prof. of Northeast Forestry University
Point 1: Furthermore the raw data ( such spectra and others) from proteomics analysis must be loaded on proteomics data base as PRIDE cPRIDE - Proteomics Identification Database (ebi.ac.uk) as requested by MIAPE (The Minimum Information About a Proteomics Experiment (MIAPE) | HUPO Proteomics Standards Initiative (psidev.info)..
Response 1: Thank you for your kind suggestion. Proteomics data is deposited at Github database, as shown on Line 506-507.
Point 2: Data can be cripted until publication, but the key for access to the loaded data should be provided to the reviewers to control the experiment.
Response 2: Thank you for your comments. There was no script for this experiment, as proteome and transcriptome data were analyzed by BioClouds Technology and Novogene, respectively.
Point 3: Line 15: The name of the studied plant Cupressus gigantea should be in italics
Response 3: Revised (Line 15).
Point 4: Line 347 delete ensuing
Response 4: Deleted (Line 387).
Point 5: Line 348 please add information on the centrifugation after ice cold acetone washing
Response 5: Added (Line 387-389).
Point 6: IAM? Specify the name of the reagent, not only the acronym
Response 6: Thank you. We revised it as “iodoacetamide (IAM)”, as shown on Line 400.
Point 7: Line 334-340 : describe all the protocols used to determine the proline , total sugars, and the activity of the antioxidant enzymes in details.
Response 7: Thank you, all the protocols are complemented in the proline , total sugars, and the activity of the antioxidant enzymes sections in the revised MS, as shown on Line 333-367.
Point 8: Line 368: explain what the normalization factor for protein identification was
Response 8: Fold-change and P values were used as the criteria for determining differentially expressed proteins, and the normalization factors were determined by literature review.
Point 9: Line 407 : describe the protocol of total RNA extraction in details
Response 9: Thank you, a few details are complemented in the RNA extraction sections in the revised MS, as shown on Line 450-459.
Thank you again for your kind work! Please contact us if you have any queries about the manuscript!
Reviewer 2 Report
Manuscript entitled “Integration of the Physiology, Transcriptome and Proteome reveals the molecular mechanism of drought tolerance in Cupressus gigantea” describes for the first-time on the chosen plant model in-depth analysis conducted by integrative approach in molecular and physiological leave with the help of two different omics. Climate changes bringing drought as one of the most devastating abiotic stressors for all leaving organisms are pushing more and more researchers to investigate how these organisms cope with it. This study has very clear experimental design covering all relevant aspects that should be analyzed morphological and photosynthetic treats, antioxidant enzyme activity, osmoprotectants synthesis, differentially expressed genes and proteins. Even more, all analysis were performed in normal, drought and rewatered conditions that is very important to see the “whole picture”, to better understand changes provoke by drought and rewatering since this could be the situations in real life. Schematic diagram of drought-induced changes in physiological parameters, genes and proteins in C. gigantea during drought stress and recovery is summarizing obtained results in clear and concise way but also pointing to the specific places where new research could be started.
Author Response
Dear reviewer:
Thank you very much for your recognition of our work. Next we will dig out the functional genes and study them further.
Yours sincerely,
Fanjuan Meng PhD,
Prof. of Northeast Forestry University
Round 2
Reviewer 1 Report
the manuscrip has been improved following reviewer's suggestion.
However its need further changes.
- Authors omitted again the name and brand of the spectrophotometer used to perform biochemical analysis. Reporting such information only one time is enough because I guess they used the same instrument for all the biochemical analysis.
- Between line 326 and 327 please insert a new subchapter as :
4.3 Biochemical analysis and then describe each item;
-The link provided for the Proteome data does not run: https:// https://github.com/lppa- 505 per/database. Only a zip file in chinese characters appeared. I cannot read what it means.
ii) the reviewer should be allowed to check the quality of the data, before the manuscript is manuscript. this is compulsary for any proteome assay.
Pride allows that check. Load you data in the suggested database and give me the key for checking.
Line 345: add a space between potassium and phosphate
Is the measured glutahione reduced or total?
Author Response
Response to Reviewer 1 Comments
Point 1: - Authors omitted again the name and brand of the spectrophotometer used to perform biochemical analysis. Reporting such information only one time is enough because I guess they used the same instrument for all the biochemical analysis.
Response 1: Deleted (Line 456).
Point 2:- Between line 326 and 327 please insert a new subchapter as : 4.3 Biochemical analysis and then describe each item;
Response 2: Revised (Line 327).
Point 3: -The link provided for the Proteome data does not run: https:// https://github.com/lppa- 505 per/database. Only a zip file in chinese characters appeared. I cannot read what it means.
- ii) the reviewer should be allowed to check the quality of the data, before the manuscript is manuscript. this is compulsary for any proteome assay.
Pride allows that check. Load you data in the suggested database and give me the key for checking.
Response 3: Thank you for your comments. We revised it as “https://github.com/lppaper/datebase”, as shown on Line 512. The zip file in chinese contains raw proteome data when decompressed.
Point 4: Line 345: add a space between potassium and phosphate
Response 4: Added (Line 346).
Point 5: Is the measured glutahione reduced or total?
Response 5: Thank you for your kind suggestion. We added a description of ASA, ASA+DHA, GSH and GSH+GSSG as shown on Line 457-471.
