Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TEMPERATURE-INDUCED CHANGES IN EGG WHITE ANTIMICROBIAL CONCENTRATIONS DURING PRE-INCUBATION DO NOT INFLUENCE BACTERIAL TRANS-SHELL PENETRATION BUT DO AFFECT HATCHLING PHENOTYPE IN MALLARDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear, unambiguous, professional English language used throughout: YES
Intro & background to show context. Literature well referenced & relevant: YES, I have added some literature citations in the specific suggestions below.
Structure conforms to PeerJ standards, discipline norm, or improved for clarity.
Figures are relevant, high quality, well labelled & described.: YES
Experimental design: Original primary research within Scope of the journal: YES
Research question well deﬁned, relevant & meaningful. It is stated how the research ﬁlls an identiﬁed knowledge gap: YES
Rigorous investigation performed to a high technical & ethical standard: YES
Methods described with suﬃcient detail & information to replicate: YES
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.: YES
Additional comments: I have added some suggestions and literature citations in the attached PDF file


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TEMPERATURE-INDUCED CHANGES IN EGG WHITE ANTIMICROBIAL CONCENTRATIONS DURING PRE-INCUBATION DO NOT INFLUENCE BACTERIAL TRANS-SHELL PENETRATION BUT DO AFFECT HATCHLING PHENOTYPE IN MALLARDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Typo checks:
line 43: alterate
line 232: affinity


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TEMPERATURE-INDUCED CHANGES IN EGG WHITE ANTIMICROBIAL CONCENTRATIONS DURING PRE-INCUBATION DO NOT INFLUENCE BACTERIAL TRANS-SHELL PENETRATION BUT DO AFFECT HATCHLING PHENOTYPE IN MALLARDS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The Ms is well written except in the abstract and at the beginning of the indtroduction English imporvemnts may be necessary.

The MS is well organized and all the relevant results shown. All tables and figures are necessary and clearly represented.

Literature is fully explored.

However, I have a problem with hypotheses and predictions. This is related to a comment mentioned by another reviewer earlier and which to my opinion is not fully answered (see later).
Experimental design: Most of the methods described are sufficient. However I miss, as far as I can see, an explanation of the phenotypic measurements in the methods section e.g. there is no explanation, information about scaled BMI or residual body mass, e.g. when and how they were measured and what is meant with it, etc.!
Another  point is whether phenotype is a proper term alternatively you may say what it is namely individual quality or condition. Phenotype frequently also implies other characteristics!
Validity of the findings: The authors produced already similar studies with other species, thus the novelty of the study is limited, but  the topic is very interesting and there is not much known yet.
This study is mixed and contains experimental and correlational parts. Thus conclusions should be still drawn with care.
Additional comments: In this study the authors experimentally examine the importance of two parent behaviours, namely partial incubation and covering the eggs during the egg laying period. Both behaviours may possible influence egg temperature and consequently  egg shell microbiome and the concentration of egg white lysozime,  avidin and consequently the amount of bacteria penetrating through the eggshell. Finally they investigate, wether there is an effect on hatching success and offspring condition. As a model species they use the mallard, a precocial bird species. According to the results, from the two behaviours, partial incubation seems to effect offspring condition whereas covering the eggs seems not important.

I have one major point, which seems to be raised already by another author ealier. I do not have the feeling that this point is answered satisfactory, at least not in the MS.
As the reviewer pointed out Lysozyme is mainly produced in the the oviduct of the female, and deposited in the egg white. Thus it is impossible that the lysozyme concentration increases after oviposition.
The authors need to deal with that point in more detail in the MS and not only in the rebuttal letter!
It is essential to explain and dicuss why you use lyozyme as the dependent variable here!!

In this context the introduction is well written and covers most of the important areas but one topic the authors may inlcude (introduction and discussion) is maternal investment i.p. related to offspring immunity.

Abstract:  English seems poor.
The first paragraph in the introduction is  rather inflated and in principle hard to understand, you may consider to simplify and reduce that part.

Statistical procedures and results are well done.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TEMPERATURE-INDUCED CHANGES IN EGG WHITE ANTIMICROBIAL CONCENTRATIONS DURING PRE-INCUBATION DO NOT INFLUENCE BACTERIAL TRANS-SHELL PENETRATION BUT DO AFFECT HATCHLING PHENOTYPE IN MALLARDS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The MS has significantly improved after the revision.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: One thing which came to me and you may mention in the MS (introduction discussion) is, that in other species, also other material than feathers is used to cover eggs (e.g. starlings), and these nest material (aromatic plants) can have strong antimicrobial properties.
This may open up new future research possibilities!


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENVIRONMENTAL CHANGES IN YELLOW RIVER DELTA WITH TERRACE CONSTRUCTION AND AGRICULTURAL CROPPING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is fluent in English and conforms to the structure of an academic paper.
Experimental design: Research question have a certain value, but the experimental design is not systematic.
For example, the experimental design did not consider the differences in crops, and there is no long-term data support；why did the author choose to do the weed survey in September instead of other representative months?
Validity of the findings: The conclusion is not well stated, and the content of the statement has little to do with the research results.
L.188: There are no related results of soil erosion to support this part.
L.190: The result of soil nutrients in the article is 0-30cm, not greater than 20cm.
L.190: There are no indicators to support the sustainability of the three land use types, and the author does not propose how to improve soil fertility.
Additional comments: Figure 1 does not clearly show the three types of land use. It is recommended to add photos or explain more clearly.
The author also needs to explain or answer several key questions:
1. Whether the input of irrigation, chemical or organic fertilizers etc. can make the local agriculture sustainable development, there is no deep discussion in the article;
2. The Yellow River Delta has a large area. What is the area and representativeness of the land use types discussed in this article?
3. Can the research content in the article support the title and conclusion?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENVIRONMENTAL CHANGES IN YELLOW RIVER DELTA WITH TERRACE CONSTRUCTION AND AGRICULTURAL CROPPING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study investigated the environmental changes result from the terrace agriculture in Yellow River delta in China. The result showed that the soil salinity has been efficiently reduced by the terrace construction. Weeds on the terrace slopes can protect the terraces with roots and rhizome. Overall, the result is interesting and provides useful information for sustainable agriculture. This paper is well organized with technical text structure and figures, but some details in describing the methods and results need to be improved.
Experimental design: The experiment overall was well designed and conducted rigorously, but some details need to complement.
1.LINE 58: “sustainability of landuse” was proposed to be evaluated, but there was no relative index on the sustainability found in this paper. Therefore, I suggested reword this sentence and remove the “sustainability evaluation”.
2.LINE 60-61: hypothesis for this study was supposed. However, the sentence ”however.......” is not a hypothesis, but a conclusion. I suggest remove this sentence. Moreover, the word “useful” in line 60 is ambiguous. Please suppose specific points (e.g. reduce salinity, improve the soil nutrients) instead of “useful”.
3.LINE 67: The field survey was conducted in September 2017 and 2018. If the field survey had been conducted twice, the year effect was not presented in the results. Author need give more details in processing the data from two years.
4.LINE 89: the manufacturer and producing place of instruments should be given (here for ST2100).
5.LINE 94-95: I suggested the soil layer can be treated as fixed factor, rather than a covariate, because the soil layers for each sample are the same and are always considered as a main factor in explaining the variation of soil properties. Thus, two-way ANOVA can be applied for testing the effect of land type and soil layers, as well as their interactions, on soil properties.
Validity of the findings: The result were explicit and conclusions were made based on the data, here’s only one point on the Figures organization.
1.Figure 2-4: Since the land type was treated as a main factor in explaining the changes in soil properties, the soil properties of different land type and soil layers can be presented in one unstacked bar chart (land type as X axis and soil layer as groups). Maybe this way is easier for readers to compare the difference among land types and soil layers.
Additional comments: 1.The title was unclear, and the key word “time” was even not studied in this research. If author wish to emphasize the “timely revolution”, the chronic changes of cropland ecosystem need to be studies. Here, I suggest use a simple but explicit sentence such as “the changes in ....on terrace cropland”

2.Author discussed the positive, negative and obscure changes in soil properties and weeds of the terrace cropland comparing with the crude flat and slope land. However, only the decrease of salinity on the terrace cropland and strong growth of weeds on slope land can be explained by the terrace construction. The increase of pH, decrease of soil organic matter and changes of soil N and P were all attributed to the fertilization and tillage, rather than the terrace construction. Therefore, I suggest the discussion can be reorganized as 1. effect of terrace construction, 2. effect of tillage. This structure can be more fit to the aim of this study.

3.Author mentioned “weeds were insufficient to compensate for the decomposition of soil organic matters in the cropland”. However, I can not find this point neither in result nor discussion. Please give more explanation on this point in the discussion.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENVIRONMENTAL CHANGES IN YELLOW RIVER DELTA WITH TERRACE CONSTRUCTION AND AGRICULTURAL CROPPING
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The experimental design has major flaws.
“ In September, the crops are harvested but weeds are left. Before it, the crops is high and immature, the farmers do not allow the investigation” is not a good explanation.
Validity of the findings: no comment
Additional comments: Figure 1 still does not clearly show the three types of land use. It is recommended to add Field photos.
Fig. 4 What are dry plant underground organs？ Need to explain in full text.
"The surveyed weed characteristics were the biomass of roots and rhizomes, species composition, life form, cover and height" is Not fully demonstrated and explained in the results and discussion section.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENVIRONMENTAL CHANGES IN YELLOW RIVER DELTA WITH TERRACE CONSTRUCTION AND AGRICULTURAL CROPPING
Review round: 2
Reviewer: 2

Output:
Basic reporting: This paper has been greatly improved from the first version, and all the comments have been solved.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME ANALYSIS AND FUNCTIONAL IDENTIFICATION OF GMMYB46 IN SOYBEAN SEEDLINGS UNDER SALT STRESS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Lin et al. identified short-term salt responsive 1235 DEGs using RNA-seq and reported the important function of GmMYB46 in salt tolerance in Arabidopsis. This submission has certain significance for soybean salt stress tolerance. However, this submission was not well prepared, and there were many writing errors. There are more than ten errors in the abstract alone!
Basic reporting
1. There are many writing specifications and English grammatical errors in the whole article. I marked some errors in the review pdf I uploaded. I suggest that an English expert revise the full text again, which will significantly improve the quality of the article.
2. Requires proper explanation of osmotic stress and ion toxicity (line 28-29).
3. Please carefully revise the reference according to PeerJ's requirements. I have marked some obvious errors.
Experimental design: 1. Short-term salt stress response and long-term salt stress tolerance are different molecular mechanisms and often have different molecular regulatory networks. In this submission, the author actually only identified soybean short-term salt stress response (only at 6h) DEGs with extremely loose DEG restrictions (p < 0.05; |Log2 fold change| > 1), not salt-tolerant DEGs. Fortunately, they claim that a short-term salt responsive DEG (GmMYB46) plays an important role in salt tolerance (at 5d and 7d). This implies that GmMYB46 plays an important role in both short-term salt response and long-term salt stress tolerance, and the author should discuss it because the number of similar genes is very small.
Validity of the findings: 2. Extremely loose DEG restrictions (p < 0.05; |Log2 fold change| > 1), add DEGs results of p < 0.01; |Log2 fold change| > 1.5 in supplementary, please feedback the number of DEGs and whether GmMYB46 is in new DEGs? Is the main annotation path the same as it is now?
Additional comments: 3. Has the author published the RNA-seq data? Please provide SRA number and add this in text!
I suggest that the author make major revisions based on the above questions.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME ANALYSIS AND FUNCTIONAL IDENTIFICATION OF GMMYB46 IN SOYBEAN SEEDLINGS UNDER SALT STRESS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. The use of the grammar structure and vocabulary needs to be improved. “Salinity is a major abiotic stress that limits plant growth and crop productivity.” It is suggested to change “a major abiotic stress”to“one of the major abiotic stress.”
2. The name of the species should be italicized in the whole article. Like Arabidopsis and Agrobacterium. Please change to the correct font format.
3. The species of the soybean used in the experiment was not informed. Please add the name of the species.
Experimental design: no comment
Validity of the findings: Fig 6C: In this picture, the expression level of GmMYB46 was firstly increased and then decreased under the treatment of mannitol compared with salt treatment, please describe it in detail and tell the reasons.
Additional comments: The section of discussion should not only describe the experimental results, but put forward the differences and improvement of the experimental results with predecessors.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME ANALYSIS AND FUNCTIONAL IDENTIFICATION OF GMMYB46 IN SOYBEAN SEEDLINGS UNDER SALT STRESS
Review round: 1
Reviewer: 3

Output:
Basic reporting: English is flawed and needs to be improved.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1. I have doubts about the author's analysis direction. According to the results of TFs, it is unwise for the author to select candidate genes based on the number of DE gene family members, ignoring the family expression abundance, in other words, why not choose AP2/ERF, bZIP, NAC?

2. In the KEGG enrichment analysis, the authors had screened several candidate genes, but some of them were up-regulated and some were down-regulated. This requires the authors to give more functional verification and discussion.

3. The author's discussion has no focus, and the genes are not systematically related. This point needs to be revised

4. In the results section, the author’s description of the results is too verbose and needs to be streamlined.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME ANALYSIS AND FUNCTIONAL IDENTIFICATION OF GMMYB46 IN SOYBEAN SEEDLINGS UNDER SALT STRESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have satisfactorily addressed all comments, the revised manuscript is now suitable for publication in PeerJ.
with kind regards,
Experimental design: no comments
Validity of the findings: no comments
Additional comments: no comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME ANALYSIS AND FUNCTIONAL IDENTIFICATION OF GMMYB46 IN SOYBEAN SEEDLINGS UNDER SALT STRESS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The use of the English language needs to be improved.
Experimental design: It is better to prove overexpression of GmMYB46 enhances the salt tolerance of transgenic soybean.
Validity of the findings: It is suggessted to improve the sharpness of the Figure 1(A).
Additional comments: The part of discussion is not profound enough. It is suggested to add the innovation and improvement of this experiment and previous experiments.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACCLIMATION OF LIVERWORT MARCHANTIA POLYMORPHA TO PHYSIOLOGICAL DROUGHT REVEALS IMPORTANT ROLES OF ANTIOXIDANT ENZYMES, PROLINE AND ABSCISIC ACID IN LAND PLANT ADAPTATION TO OSMOTIC STRESS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: In this manuscript, Ghosh et al. studied the response of the liverwort Marchantia polymorpha to physiological drought.

I have a major concern regarding the research question and the way it is presented. The author use here Marchantia polymorpha as a model and present it as "the first land plant" which is absolutely incorrect. From this hypothesis the author conclude that their finding in Marchantia polymorpha represents the ancestral state in embryophytes, which is again incorrect and misleading.

I suggest the authors to entirely rewrite the manuscript for that important aspect. A good read before rewriting would be Delaux et al. 2019 (10.1016/j.cub.2019.09.044).

For instance:
- "diverging land plants" I assume the authors mean "early diverging land plants", which is actually a term to avoid as early diverging as to be used as a comparison with a "later diverging" group. This is irrelevant here
- "Basal land plants" cannot be used either.
- l 77-78: "bryophytes.. are considered the first land plants" this is wrong. The first land plants died more than 400 million years ago. bryophytes are as "evolved" as flowering plants or ferns. Please reformulate.
- l382: "..in basal representatives and today's land plants". This sentence would suggest that marchantia polymorpha is actually a fossil.

Material and method
"we searched the gene in all representative of terrestrial plants" please rephrase as the BLAST search was restricted to less than 10 species.
Validity of the findings: Given that I am not an expert in the physiological measurement conducted by the authors it is difficul for me to comment on that.

The phylogenetic analysis conducted on the proline biosynthesis gene seems reliable, although more details on the substitution mode etc.. would be an important addition.

As stated above, concluding on the ancestral character based on Marchantia polymorpha is not relevant. The authosr should compare with angiosperms/vascular plants to draw evolutionary hypotheses.

I would find interesting to compare the results from this paper with the recent paper by Wu et al. 2021 (10.1038/s41477-021-00929-7) that studied another stress (salt) in Marchantia polymorpha.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACCLIMATION OF LIVERWORT MARCHANTIA POLYMORPHA TO PHYSIOLOGICAL DROUGHT REVEALS IMPORTANT ROLES OF ANTIOXIDANT ENZYMES, PROLINE AND ABSCISIC ACID IN LAND PLANT ADAPTATION TO OSMOTIC STRESS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ghosh et al treats gemmae and gemmalings of the liverwort Marchantia polymoprha with one concentration each of sucrose, mannitol, PEG and ABA. After some time, the phenotypic and molecular changes are interpreted as drought responses. Growth, chlorophyll levels, enzyme activities, etc are measured.

First of all, this manuscript needs language editing. Many times in the manuscript editing is needed for clarity, as I am not sure what the authors try to say.

Second, the framing of the study in the introduction is very poor. The introduction lacks new references. There must be lots of drought studies in liverworts and mosses that would help the authors frame their own work. Please cite them appropriately.

The results section is very short considering there are 5 figures with original data. This section could be expanded by clearly stating what was done and how, plus including references, and maybe also better motivating why some experiments were done.

The conclusions and speculations outreach the limited results presented. The authors need to read published papers of relevance for their study and cite them as appropriate throughout the manuscript.

The discussion is much longer than the results, and repeats much of the results. Present data in the results and put them in context in the discussion.
Experimental design: The authors use Suc, Man and PEG because other papers have used these treatments. If all three works as “drought” why is there a significant difference between PEG and the other two treatments in many of the experiments?

I don’t like that the authors grow plants on sugars and then write about drought treatments. There should be plenty of water in the B5 plates, and some of the experiments is done in liquid media. Wouldn’t it be better to write about sucrose, mannitol and PEG treatments? The authors can explain and discuss why their experiments should be interpreted as “drought treatments” in the discussion.

Are the plants alive after Suc and Man treatments in fig 1A? They look dead. Would they start growing normally if transferred to a normal B5 plate with nothing added?

What accessions and sexes have been used in this study? Have a single accession and sex ( = a single genotype) been used for all experiments? If so, ABI1 is reported to be located on the sex chromosomes and therefor there could be differences in ABA-mediated stress-responses between sexes in M. polymopha.

The tree is made using NJ. Not sure that method is good enough, especially considering that the tree looks poorly made (it has very low support values on many nodes). Is the tree rooted? Much more details on tree construction is needed in the M&M.

The authors use only 3 replicates in most of their experiments. I am not sure growing three genetically identical plants (clones) next to each other on the same plate actually counts as three biological replicates. Maybe there is something with that specific plate that affects the experiment. I would probable treat this set up as three technical replicates. Having clones on different plates, or even better having different genotypes of wt on the same plate, using three identical plates, would be my biological replicates if I would do this type of experiment.

I am concerned about the photo of “normal” plants in Figure 1A and Figure 6. These plants do not appear to grow normally. This looks a lot like a plant that is stressed or is receiving too much blue light and too little red light (the thalli appear to be elongated and twisted?).

The authors say the plant grow for 15 days, but the plant in fig 1A must be much older than 15 days? It has bifurcated three times. I have never seen this type of growth speed for plants that grow in white light in 16/8 photoperiod at 22C.

Marchantia gemmalings growing in liquid medium/water must be water stressed. Then the authors add Suc/Man/PEG, and suddenly the plants are “drought treated”. Wouldn’t it be better to compare drought stress to no stress, rather than another type of stress.
Validity of the findings: The raw data is provided. But I don’t see much information of the statistical analyses in the text. Also see the comment below on using numbers like 123.56%.

The statistical analyses appear to be ok, even though I don’t understand why and when different methods are being used. However, there is a problem with support in the phylogenetic tree. Branches that are not supported should be collapsed. The method for calculating branch support needs to be included.

As I wrote above, I am not sure if this manuscript is using three biological replicates (says something about biological variation) or three technical replicates (says something about how good the method is). The error bars are very small, so I would assume this set up is more to be considered as technical replicates than biological replicates.

If I understand the M&M, two different statistical test have been done. When and why were the two different tests used? This should be indicated in the figure legends or results section. Also, would be good to provide the P-values, not just stating that it is significant or not significant.
Additional comments: Below are some comments on specific parts of the text:

Line 21: Why?

Line 22: What is an “evolutionary component”?

Line 26: improper use of semi colon

Line 40-42: Inaccurate interpretation of data. M. polymorpha did not exist during the early stages of plant adaptation and evolution. The authors must revise their hypothesis and use an accurate phylogeny over land plant evolution.

Line 44-45: So they were never stressed before global warming and environmental deterioration?

Line 46: “Plants” include lots of different algae, which are not sessile.

Line 53 and later: Use “land plants” instead of “plants” if you mean land plants.

Line 77-78: This sentence need more work. And extant bryophytes are not the first land plants. What is a basal land plant, and why are extant bryophytes basal? I think the literature is becoming more and more clear about the use of inappropriate terms like “basal plants”, “lower plants”, etc. It is important to use proper terminology to not confuse the reader.

Lines 78-80: Sentence need more work.

Line 81: What is an early land plant? Maybe good to not use several different terms (of which some are not appropriate to use) for the same thing.

Line 81-83. Use commas to make sentences better structured.

Line 84: Here is another “early plant”. Why not just wright “algae”, if the authors mean algae colonized land.

Line 86-87: Is this really correct. Who says this?

Line 88: Too many commas.

Line 91-93: This is not the current view on land plant phylogeny. The authors need to stop using old and outdated papers as reference. There are several very recent papers on land plan phylogeny that should be easy to find.

Line 95: Gemmae is plural. Should be “gemma cup”. The gemma cup is not the asexual reproductive unit. The gemmae inside the cup are. Not all liverworts have gemma cups or gemmae.

Line 99: There are newer references. Please use proper references.

Line 102: No, current data clearly shows liverworts are not sister group to other land plants, or the earliest representative of land plants.

Line 106: no s in the end of liverwort.

Line 146: Place the phylogenetic analysis under its own heading.

Figure 1: The control plant in figure 1A doesn’t appear to grow normally. Are the plants stressed? Something might be off with the growth conditions. Also, the plant in fig 6 looks very strange. Might be too warm or too much/little light of a specific wave length?

Figure 1: Have the dormant gemmae been taken from cups and placed directly on the plates with treatments? If so, can the authors distinguish between effects of delayed germination of gemmae and effects on growth retardation in gemmalings, in figure 1?

Figure 1: There is no time aspect, like a measurement of growth speed. Therefor it is impossible to say if this is delay of growth initiation (release of dormancy and germination) or growth retardation (slow growth from the apex of the gemmaling).

Figure 1: Why are these specific concentrations used? There is no investigation of dose effect (that the severity of the phenotype correlates to the concentration of the chemical added), and there is no reference to a previously done study of dose effect of Suc, Man and PEG on gemmae and gemmalings.

Figure 1: Wouldn’t 0,2 M sucrose be expected to have the same effect as 0,2 M mannitol?

Line 207: Is there a statistically significant difference between Suc and Man in fig. 1? If not the authors can’t say that it is.

Line 217-219: Put the results in better context. Refer back to what is known from Arabidopsis or other relevant plants

Line 233: What enzymes are these? Please write the full names at first mention. Also mention why they are relevant.

To say that something is increased by e.g. 137.76 % is very exact. Have the authors actually done their experiments in such a way that they can give numbers this exact?

Line 242: in the end of the results paragraphs the authors summarize using the wrong tempus. Our results suggest…

Paragraph starting at line 247: What is the purpose of the phylogenetic tree? Because a phylogenetic tree is not used for what the authors says it is in this paragraph.

Figure 4: The authors need to look at their tree and interpret what they see. The authors should include their alignment (which should include sequences that have been trimmed properly) as a supplemental file as this is important for the interpretation. Also, what do the different numbers in the tree show? Is a number of 30 relevant (if so, why?) or should that branch be collapsed? Why are different versions (I assume splice variants) of the same gene included in the tree? The authors need to learn how to build and present a phylogenetic tree.

Line 257: What? Also, do the authors use “e.g.” when they actually mean “i.e.”?

Line 257-259: What do the data actually say, and what is speculation? The authors must take care not to overinterpret their data, and the authors must be very clear what is speculation and what is interpretation of their data.

Line 263: “Drought exposure”… No. Exposure to different concentrations of Suc, Man and PEG.

Figure 5: The authors need to provide a reference saying that Evans Blue work on M. polymorpha tissues in the way the authors claim.

Figure 5: The photos needs to be comparable and some sort of quantitative analysis on evans blue staining should be done. The photos should be of similar brightness, zoom, etc.

Line 401, etc: I hope the authors are aware that there are previous studies showing that ABA and ABA-signaling components have a role in M. polymorpha? Cite the available literature.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ACCLIMATION OF LIVERWORT MARCHANTIA POLYMORPHA TO PHYSIOLOGICAL DROUGHT REVEALS IMPORTANT ROLES OF ANTIOXIDANT ENZYMES, PROLINE AND ABSCISIC ACID IN LAND PLANT ADAPTATION TO OSMOTIC STRESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this revised version the authors have clarified a number of points raised during the first round of review.

However, the main issue has not been fixed appropriately. The wording is still approximate when describing liverworts and the evolutionary context.

For instance “Bryophytes, which include mosses, liverworts, and hornworts, are a monophyletic group of the earliest land plants, with mosses and liverworts belonging to their own clade (Setaphyta) and hornworts being sister to other land plants” (L85) contradict itself. If Hornworts are sister to other land plants, then Bryophytes do not form a monophyletic clade. In the same sentence “earliest land plants” again suggests that Bryophytes are some sort of fossils.

I encourage the authors to carefully edit the manuscript. I also agree with reviewer 2 that the presented data should be better compared to the existing (recent) literature on the topic. Citing these papers is not sufficient. I appreciated for instance to see Wu et al. 2021 cited as I proposed in my previous review, however the authors should discuss their result in light of that other paper.
Experimental design: The experimental setup is now properly presented.
Validity of the findings: The presented data seems solid.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MTDNA SPECIES-LEVEL PHYLOGENY AND DELIMITATION SUPPORT SIGNIFICANTLY UNDERESTIMATED DIVERSITY AND ENDEMISM IN THE LARGEST NEOTROPICAL CICHLID GENUS (CICHLIDAE: CRENICICHLA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: In my opinion, the writing of the paper is not clear enough and some ideas are repetitive along the manuscript. For instance, a sentence referring to the sample size of the study (lns 33-36): "mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus six out of 36 nominal synonyms plus over 50 putatively new species)", is repeated 10 times along the manuscript.  In the introduction section, the fact that Crenicichla is the largest genus of Neotropical cichlids is mentioned three times. Another example, only in the introduction, the name Crenicichla appears 43 times!.  I understand that this is the subject of the study, but that make writing too repetitive and difficult to follow.

Even though English is not my first language, I found several places along the manuscript very difficult to follow, so I would recommend that a native English speaker revise the manuscript and determine all the aspects related to writing.

Regarding the information in the introduction section, I suggest to delete some parts. The list of species included in each species group within Crenicichla is unnecessary and can be referred to an Appendix solely. The same is true for the list of nine species of Teleocichla. Sometimes the authors refer to the genus Crenicichla as the largest in South America, and sometimes to the richest.

My suggestion is to re-structure the entire paper and try to make it more clear, and I also suggest to have an English speaking person editing the paper.
Experimental design: In my opinion the research question is well-defined.  The authors try to understand the species diversity in a highly diverse group of freshwater fishes. Their results show that the diversity is underestimated. Again, the problem is the writing and how ideas are expressed repeatedly. For example, in lns 230-233 the authors  outline the sampling, but in the preceding paragraph (lns 218-223) it was already mentioned. No methods of euthanasia are referred, and this is important since they include 681 specimens. The authors refer to the fact that collecting was supported by the Administración de Parques Nacionales and Ministerio de Ecología y Recursos Naturales Renovables, is that in Argentina?, and if so, why about all the other countries?. It is also mentioned that specimens were collected through a network of cichlid hobbyists who kept animals during 10 years. Did they have collecting permits to sample in South America?

Analyses regarding DNA sequencing and phylogenetics are ok. However, they are not consistent.  It is mentioned that dataset was analyzed through Bayesian inference, maximum lilkelihood and maximum parsimony. Figures only depict the results of BI and in the Appendix, the ML analysis performed in RAXML. The single-locus species delimitation methods are described although there is no mention about the differences between mPTP and bPTP
Validity of the findings: The results obtained by the authors are meaningful. The problem, again, is the way the results are written. It is confusing the way ideas are presented.  For example, in lns 377-380 authors said: "Since we included only 77 out of 105 presently recognized valid species and did not include a completely exhaustive areal sampling the minimum number of species in Crenicichla is more likely higher, at least 174 (and up to 232 based on the present sampling; Fig. 3).".  Maybe I am wrong, but the sentence is confusing. The same happens with the entire paragraphs of lines 390-401.

One idea of concern is that authors seem to validate the work done by hobbyists which recognize species of cichlids without a formal diagnosis and description.  I understand that the experience of aquarists is big, but we have to be careful about that.  I understand the the progress made by professionals is not "as large" as that presented in cichlid hobby literature, but I would warn about giving large support to that literature. Actually, in the discussion, authors provide a review of the putative new species previously proposed in the cichlid-hobby literature and that based in their own results through species delimitation analyses. Do not get me wrong, I am not implying that the experience of hobbyists is useless, but is has to be taken with caution.

I would suggest by starting the results presenting the evidence from the phylogenetic analysis and make it clear if that is a concatenated analysis, or is the analysis of each of the 2 mitochondrial genes separately, and define whether it is the result of ML, BI or MP.  Then move to explain the species delimitation methods and only present the overall result trying to avoid the use of so many names while describing.  See the last paragraph of results (lns 426-435). In 10 lines, the word group is used 22 times!.  That makes reading very hard.

Regarding the phylogenetic results, I would insist in showing if that is the result of a combined analysis of the 2 markers.  And also, I wonder why Fig. 2 does not present the outgroups referred in the methodology (Astronotus ocellatus and Satanoperca jurupari)?.  Is the use of the "groups" name absolutely neccessary?. I think the use of so many names is what makes reading difficult. One of the results indicate that each group is monophyletic, but what does that mean?, what is the point of having a name for a subgroup if all of the belong to Crenicichla?, and then, if removed authors avoid confusion by talking about groups forming subclades and then grups subsumed to other groups, etc.

Another recommendation I would like to make is to shorten the discussion is the species diversity section. Is way too long.  My opinion, to make it more clear is just to present an overall description of the recognized species by the delimitation methods and not talk about each group in particular and then close the paper with the section of underestimated neotropical fish diversity which, to me is very relevant.

Finally, nothing is discussed about the validity of the species delimitation results.  There is a vast literature out there on the problems associated with the use of such methods in describing biodiversity, especially in metazoans.  Some methods tend to overestimate the species diversity, and some are dependent on sample size.  This kind of arguments need to be discussed at least briefly in the paper to present a string case of why the methods of choice recovered the "true" history.
Additional comments: I think the results of the paper clearly indicate what the authors mean to show: a significant underestimated diversity in the most species-rich genus of cichlid in South America. This adds a large amount of information to the study of cichlid evolution and diversification. As they also said, this study  shows that "DNA study and other genetic tools are powerful complementary methods for uncovering fish diversity and highlighting groups in need of taxonomic revisions".  My majos criticism is that the writing is not good enough to present the large amount of information, and that is why my recommendation is to try to make it more concise, to avoid repetitive sentences, and to try to use the less number of names, so readers can follow the main ideas. So, in my opinion, if authors are willing to re-write the paper , have and English specking person reading and editing, and make a more concise presentation of fact, the paper has the potential to be published.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MTDNA SPECIES-LEVEL PHYLOGENY AND DELIMITATION SUPPORT SIGNIFICANTLY UNDERESTIMATED DIVERSITY AND ENDEMISM IN THE LARGEST NEOTROPICAL CICHLID GENUS (CICHLIDAE: CRENICICHLA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the present study, the authors gathered an impressive number of samples of species of Crenicichla and Teleocichla and this is without a doubt the strongest point of the study. On the other hand, the authors used only fragments of 2 mitochondrial gene encoding protein genes in their analysis of species discrimination and date, which represents a very weak point of the study. This scenario (many species and few data) makes the study extremely questionable because much of what is presented and discussed is based on topologies without statistical support. In this way, I suggest that the attempt to date be eliminated since with the amount of available data it is not possible to make a robust phylogeny for the genera and that the methods of discrimination of species be revised in order to avoid speculation as to the formation of groups and relationship issues.

The introduction is well written and I suggest the addition of references in the phrases of the lines 76-79, 103-105, 171-180, and 200-207.
Experimental design: In the Line 103 is cited 96 valid species, line 219 = 105 sp, line 371 = 96 sp.  The authors should decide which number is the true for Crenicichla.

In Material and Methods the authors says that samples were collect under permit of the Administraci.n de Parques Nacionales and Ministerio de Ecologia y Recursos Naturales Renovables (permits nos. NEA328 rnv3 and Res: 509/07) that I suppose is an Argentina authority. How about collections in other countries?

In the paragraph starting in the line 272 authors justify the use of two genes but both these genes are protein coding genes that evolves at more or less the same rate and are not able to solve correctly the relationships among groups that evolved very recently or are very old. When the see the trees presented (figures 2 and 3) it’s possible to corroborate this since most of the nodes do not present statistical support.

Why authors did not use other popular species delimitation method as ABGD?

In the line 317 the authors says “The first 10% of trees from each run were discarded as burn-in.”. This is not correct since it’s important to discard all trees found before the stabilization of the asymptote curve.
Validity of the findings: As described above the reduced amount of data makes this study very questionable considering the low statistical support of the trees. All conclusions based on this kind or result is also questionable.
Additional comments: In general the study is very interesting but the finds should be reanalyzed in order to reach to a more sustainable conclusion.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MTDNA SPECIES-LEVEL PHYLOGENY AND DELIMITATION SUPPORT SIGNIFICANTLY UNDERESTIMATED DIVERSITY AND ENDEMISM IN THE LARGEST NEOTROPICAL CICHLID GENUS (CICHLIDAE: CRENICICHLA)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English used in the MS is professional, although some parts require to be more concise.
I considered that the figures required to be better formatted.
The final conclusions of the MS required a strong review in terms of their limitations considering the markers used, and also the main goal of the study fails to completely describe the study.
Experimental design: I consider the MS a valuable contribution to PeerJ, particularly considering the extensive sampling effort of the study, together with the relevance to the phylogeography of the group, however, some reviews are required.
Validity of the findings: The MS requires to clearly state their major findings in contrast to previous studies with larger data sets. Moreover, some conclusions require revision particularly considering the limitations of the markers used, and also the main goal of the study fails to completely describe the study.
The final part of the MS is verbose and at some points not very well organized, possibly a figure could help the authors organizing this section.
Additional comments: The most important concern is related to the inconsistencies observed between the BI and RaxML reconstructions between the species groups with the mitochondrial markers used in the study. In this regard, the authors suggested that markers' saturation could be the main reason for these inconsistencies. However, there is no proof of this saturation in the analyses. Since this is a major goal of the study, I would recommend to the authors, to possibly include some nuclear information that could help them to suggest a more robust hypothesis about the relationships between the two species groups.

Moreover, interestingly the authors present in the MS the BI topology, rather than RaxML, being the latter congruent with the genomic data, thus, recovering Teleocichla nested within the Crenicichla.

Moreover, there is no sense that the authors only described as a major goal of the study the relationship between Crenicichla and Teleocichla, instead of testing the phylogenetic relationships between the major species groups described in the manuscript. I consider this a major point to better describe the main goal of the study.

At some parts of the MS it is difficult to understand the major differences, or systematic advances of the present in contrast to the previously described studies: Piálek et al. 2012 and Burres et al, 2018. Thus, I strongly recommend to the authors to clearly specify in which way this MS corresponds to an improvement of the previous phylogenetic analyses published in the group, particularly considering that some of the major differences could be due to the markers resolution differences, this is particularly relevant in the relationships between Saxatilis, Lugubris, and Acutirostris.

Moreover, the reciprocal monophyly of some groups as Acutirostris group clearly exemplifies the mitochondrial markers resolution limitations, thus, I strongly recommend to the authors, in order to give stronger support to their conclusions, and advance in the knowledge of the group, to include the available nuclear information in their analysis, and in the species delimitation. Otherwise, I found that the MS could quickly become obsolete, in terms of species delimitation, recognizing some paraphyletic groups, and questioning the validity of the study.

Finally, the last part of MS with a short review of the putative new species, I found this part particularly controversial, since as the authors describe there are some troubles with the markers’ resolution.
Moreover, at some parts the divergence times or biogeographic barriers are considered as additional criteria in the species recognition, for example:
541 Our analyses demonstrate that these and most other
542 widespread species are an illusion as explained above and that they are actually
543 species complexes composed of allopatric/parapatric species that have in most
544 instances been separated for millions of years.

However, it would be relevant to clearly specify if these species are also supported with previous studies using genomic data. Moreover, a more robust taxonomic proposal should be considering a combination of nuclear and mitochondrial markers, in this regard, I suggest to the authors to better describe the biogeographic patterns observed in their study, and consider restructuring the final part of the MS.

The last part of the MS considering the underestimation of the species diversity, I consider this part also problematic, particularly considering the wide evidence of DNA barcoding overestimation of the diversity (Song, H., Buhay, J. E., Whiting, M. F., & Crandall, K. A. (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the national academy of sciences, 105(36), 13486-13491). Similarly, to the previous suggestion, I would recommend to the authors to tone down their conclusions in this sense. Even some parts of this section are valuable to discuss (as the extensive sampling of the present study, or cryptic diversity in the group).

Minor comments:
I found the figure captions somehow confusing and difficult to follow. Also in some of the figures, the information is not well organized. For example in the Figure 2 caption, there is a large description of the image, however, there is no description of the different methods used in the species delimitation. In the figure the colors used in the species delimitation are not clear, this is particularly confusing in figure 6 where more than half of the topology present a gray color but four species are mentioned at the right side of the image (i.e. C. missioneria, C. igara, C. hadrostigma, C. celidochilus).

In the L134, the authors present a list of species included in the study I recommend them to include them in a table.
L.161 please review the phrase.

L200-207, in the major goal of the study, are not included the rest of the species groups included in the study (e.g. Wallaci among the others).

In figure 1, the points could be accordingly to the species groups, since apparently there is clear vicariance among the species.

L230, please clearly specify how many individuals were considered for each species recognized, since the delimitation methods are sensitive to the sample size.

L244, please include the correct codes corresponding to the vouchers.
L323, the description of the molecular clock is poorly described, please clearly specify which were the priors used (e.g. mutation rate).

L368, please specify the number of samples per species.

L424, please clearly specify the inconsistencies among the different methods applied.

L451, this phrase requires revision, particularly since the difference in the relationships between Crenicichla and Teleocichla, could be related to the lack of resolution of the markers used, as was mentioned in L455. Thus, as I mentioned before, it could be important considering to include the nuclear data, in order to contrast the mitochondrial information.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MTDNA SPECIES-LEVEL PHYLOGENY AND DELIMITATION SUPPORT SIGNIFICANTLY UNDERESTIMATED DIVERSITY AND ENDEMISM IN THE LARGEST NEOTROPICAL CICHLID GENUS (CICHLIDAE: CRENICICHLA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: I consider that the English used is clear and professional.
The literature is sufficient in the field.
The article requiere a review in the order of some sections (i.e. Methods), and review in the Discussion, which some parts seems more like results than discussion.
The study represent a relevant study due to the extensive sampling and for sure is relevant from a systematic point of view for this highly diverse group.
Experimental design: -The study represents a relevant contribution for the journal.
-Despite to the use of two mitochondrial markers, the study sampling clearly overcomes some limitations, highlighting the necessity of a wider sampling of some particular groups and/ or regions, in order to increase our knowledge on this group.
-I consider that the study is rigorous, but requieres a better description of the collecting permits from Brazil and Guianas samples.
-I consider that the methods a well described.
Validity of the findings: The study is meaningful.

Yes, the data is robust and well analyzed.

Conclusions are well stated.
Additional comments: MtDNA species-level phylogeny and delimitation support significantly  underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla) (#57123)

Authors: Oldřich Říčan, Klára Dragová, Adriana Almirón, Jorge Casciotta, Jens Gottwald, Lubomír Piálek

I consider that the review made by the authors considerably improved the description of the study, which overall describes a greater diversity within the genus Crenicichla than previously reported. On the other hand, the authors make a detailed description of the species groups, with some possible implications for the taxonomy that could be further explored.

However, I consider that the document still has some problems of missing information, or even lack of order in some parts. Particularly in the methods section, I consider that it is important that the authors describe with more seriousness the import-export permits of the species from Brazil and Guianas, because precisely those regions are among the most extensively sampled in the study, and some taxonomic implications are clearly based in the reliability of the locality of origin of the samples (for example L392-401).

On the other hand, it is important that some sections of the methods are organized, in this regard, markers used are described first than the methods used to obtain the DNA.

Finally, in the discussion, some paragraphs are more results than discussion (L597-611).

Minor Comments:
species-like groups, if it is a boundary, species numbers, the other resulting term ambiguous.
L83: and a large leftover.
107: ‘the best review’, this phrase requires a better explanation, since it could be relative to other studies, based on particular criteria, but all aspects, again this phrase is vague.

L136: "True species", this also does not seem exact, since it is not a question of true or false, but complete or exact, check it.

L318 - Specify the distribution used in the node calibration.

Sometimes the complexes are in subtitles and sometimes they are not (L581, L588, L597, etc.)

L625: sensu lato in italics
L627: sensu stricto in italics


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The language of this manuscript is crude.
Experimental design: No comment.
Validity of the findings: No comment
Additional comments: This commentary performed transcriptome sequencing of female and male flower buds at different development stages. And found that hormone signal transduction pathways play an important role in the sex differentiation of J. mandshurica. Then the gene expression patterns were verified by q-PCR, and endogenous hormones were determinated.
Overall, the idea of the manuscript is clear. However, some issues still need to be improved:
1.	The language of this manuscript is crude, some descriptions are difficult to be read, and an embellishment on the language is required.
2.	In lines 39-43, first you said dioecious mating system is not common in flowering plants, but then you said only only Batulaceae, Corylus, Juglandaceae, Carya, Juglans, and Cyclocarya are woody plants with a monoecious mating system. The sentence reads contradictory. Please recheck this sentence to make it clear.
3.	All the text in the manuscript need justify align. A space is required before the reference in the manuscript in lines 38, 40, 44 et al.
4.	Figures 2 displayed the original data, which should be removed to supplementary materials. Figures 3,4, 5 are too simple and could be integrated into one figure. The contents of figures 7 and 7 are similar and thus should also be integrated into one figure.
5.    The quality of Figure 9, 10 is poor, please provide the original figure.
6.     Figure 9, the RNA seq data also need an error bar.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper is general clearly describe and easy to understand. But there still some sentences need to be rewrtie or modified. Such as: 1.In the introdcution part line 70 to line 74. I was confused by this sentence.  2. In the abstract, line 29-line 30, ARF and SAUR were expressed differently in the auxin signaling pathway. I don't understand this sentence.
Experimental design: This experimental design is well defined and meaningful.
Validity of the findings: More data details need to be added. And the conclusions need to be developed.
Additional comments: This paper is well designed and the result seems to be very intresting. I beleived this paper could be improved a lot. I suggest to add more information about the hormone synthesis genes expression relevant to the hormone detection. Meanwhile ,some figures need to be improved. Such as the heatmaps. The hormone detection result is very important, this should be discussed in the discussion part and should be mentioned in the abstract. The sample collection should be described more clearly, since it is very improtant. The file containing all genes' expression data, annotation and symbols should be provied.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 1
Reviewer: 3

Output:
Basic reporting: Authors used male and female flower buds of J. mandshurica at the physiological differentiation stage. Illumina-based, transcriptome sequencing was performed, and the quality of the sequencing results was evaluated and analyzed. Findings are not extremely novel, but they do perfect fill a regional knowledge gap.
Experimental design: no comment
Validity of the findings: The introduction is well-written and concise. The methods are exceptionally clear compared to most manuscripts I've reviewed on the subject. Results are well constrained and the author does not over-extend the discussion or conclusions. I do not often compliment manuscripts in review, but this is one of the most straightforward manuscripts I have read in a very long time and that was refreshing.
Additional comments: Before the paper is accepted, there are several questions should be considered:
1. The details of geography distribution of J. mandshurica should be mentioned.
2. The future work in Discussion section need to be added.
3. The Conclusion section should be enriched, and the last sentence need to be deleted.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors addressed the questions well.

For Figure 11, the statistical analysis needs to be added. Or change the figure into a table containing
all the information


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSCRIPTOME-BASED ANALYSIS OF THE HORMONE REGULATION MECHANISM OF GENDER DIFFERENTIATION IN JUGLANS MANDSHURICA MAXIM
Review round: 2
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENE POLYMORPHISMS IN ULK1 AND PIK3CA ARE ASSOCIATED WITH THE RISK OF MICROSCOPIC POLYANGIITIS IN THE GUANGXI ZHUANG AUTONOMOUS REGION IN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript “ Gene polymorphisms of ULK1 and PIK3CA are associated with risk of microscopic polyangiitis in the Guangxi Zhuang Autonomous Region in China” (#62693) addressed a rare type of vasculitis. The authors try to find a connection between SNPs in autophagy-related genes, such as ULK1 and PI3KCA and the susceptibility to microscopic polyangiitis.
The study included 208 eligible patients with microscopic polyangiitis and 211 healthy controls.
The manuscript is well written, includes a sufficient introduction. However, in this part is not clearly presented the authors` hypothesis, why they have focused exactly on these genes in their research.
The structure of the article conforms to the format of the journal. Figures are relevant to the content of the article, appropriately labelled. Raw data are shared, but they are partial and incomplete. These are not all the data based on which the analyzes in the article are made.
Experimental design: The study was conducted in conformity with the ethical standards in the field and the authors presented in supplementary data. Methods are described in detail.
I think that "Clinical Characteristics of study population" from section "Results" have to be moved to the section "Materials and Methods".
Validity of the findings: All underlying data are presented appropriately. There are discrepancies in the presentation of the results in the text and in the tables. There are not any results about the functional activity of these SNPs. Table 5 is difficult to trace and should be divided into three tables - by age, gender and ethnicity.
Conclusions are general. The study is descriptive but does not give any answers to finding even speculative ones.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENE POLYMORPHISMS IN ULK1 AND PIK3CA ARE ASSOCIATED WITH THE RISK OF MICROSCOPIC POLYANGIITIS IN THE GUANGXI ZHUANG AUTONOMOUS REGION IN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript utilizes single-nucleotide polymorphism (SNP) analysis to investigate the associations between the autophagy-related genes ULK1, PIK3CA and the autoimmune disease-microscopic polyangiitis (MPA) in patients from the Guangxi Zhuang Autonomous Region in China. Through series of data analyses, they revealed two risk loci in ULK1 and one protective locus in PIK3CA for MPA. This idea behind the manuscript is meaningful for both basic and clinical research, however, there are certain gaps and misleading parts in result and discussion, which need to be further improved.

Major Concerns:
-line51-53, the result said “ULK1 haplotype (G-T-A-G-A) and PIK3CA haplotype (C-G) are associated with an increased risk of MPA, and PIK3CA haplotype (T-G) is associated with a reduced risk of MPA.” This conclusion mainly comes from the Table 4, the haplotype of ULK1 is G-T-A-C-G-A, not “G-T-A-G-A”. And it was associated with a reduced risk of MPA, not “an increased risk”. Please check the result carefully and draw the correct conclusion.

Minor Concerns:
The English language should be improved to ensure that an international audience can clearly understand your text. Some examples where the language could be improved:
-line44 & 124 : “high-through sequencing” should be “ high-throughput sequencing”.
-line47: “The single-SNP analysis detected significant differences in genotypic distribution in two SNPs between two groups: ULK1 rs4964879 (p = 0.019) and PIK3CA rs1607237 (p = 0.002).” please reorganize this sentence.
-line50: “reduced MPA risk” should be “ a reduced MPA risk”.
-line67: “;” should be “,”.
-line71: “A European study showed that PR3-ANCA is associated with HLA-DP that encodes SERPINA1 and PRTN3, where MPO-ANCA is associated with HLA-DQ (5).” Please refer to the original article, and reorganize this sentence, for example, should be the genes of anti–proteinase 3 ANCA encode SERPINA1 and PRTN3. “where” should be “while” in your sentence.
-line153: “consisted of 128 females and Han nationality population”, should be “consisted of 128 females and 155 Han nationality population”.
-line159: “the allele frequencies of gene PI3KCA rs1607237 (C＞T) were significantly different between the MPA group and the control group (p = 0.013).” Based on the Table 2, the p value should be 0.011?
-line182: (Table 3) should be (Table 4).
-line200: “could increase MPA risk” should be “, which could increase MPA risk”.
-line235: “The knockdown of ULK1 in HEK293 cells was reported sufficient to inhibit autophagy response”. please reorganize this sentence.
-line278: “loci” should be “locus”
Experimental design: The authors mentioned the selection criteria for the SNPs in ULK1 and PIK3CA genes, the sites were located in the functional region. So, are there any solved structures for the proteins encoded by ULK1 and PIK3CA genes. If so, could the author further discuss the potential reasons why the SNPs in ULK1 and PIK3CA genes have different affects on MPA based on the protein structures. If not, are there literatures talking about the relationship or signaling pathways between ULK1 and PIK3CA-related proteins, please discuss it. The connections between ULK1 and PIK3CA genes, excepting they are both autophagy-related genes, could further explain the purpose of this study and experimental design.
Validity of the findings: In the conclusion, the authors mentioned basic research is needed to confirm their conclusion, which also should be one of the limitations in this study. Please discuss it in “Discussion Section”. For example, what types of basic research are needed to confirm your results, which could provide guidance for further studies.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENE POLYMORPHISMS IN ULK1 AND PIK3CA ARE ASSOCIATED WITH THE RISK OF MICROSCOPIC POLYANGIITIS IN THE GUANGXI ZHUANG AUTONOMOUS REGION IN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have sufficiently addressed my concerns.
However, the authors should carefully check the manuscript again to make sure professional English used throughout. For example, there are still wrongly written word "PI3KCA" in table 2 and 4.
Experimental design: The authors have sufficiently addressed my concerns.
Validity of the findings: The authors have sufficiently addressed my concerns.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: STUDYING SUICIDE USING PROXY-BASED DATA: RELIABILITY AND VALIDITY OF A SHORT VERSION SCALE FOR MEASURING QUALITY OF LIFE IN RURAL CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a very well-written, succinct paper regarding the use of the QOLS-6 involving 242 elderly suicides and matched controls in rural China, with informants for both and direct interviews for the controls.  The study has been well-designed and supports between group comparisons--suicide-informants v. control-informants, and controls v. control-informants. Its results provide confidence in the use of this measure!

There is nothing specific in the current manuscript that I would critique, in terms of methods, data acquisition, analysis, or interpretation.  However, the authors miss a key potential element when not comparing results for men and women, to assure the same high level of confidence that is evident with the overall results.  While one might expect findings to be similar, we know that men and women are very different in their communications and interpersonal interactions, and it would appear that the sample size would support exploratory sub-analyses.

The use of English in this manuscript is quite good.  I do see one error on line 155...presumably, "wildly" is meant to be "widely."
Experimental design: As above
Validity of the findings: As above
Additional comments: As above


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: STUDYING SUICIDE USING PROXY-BASED DATA: RELIABILITY AND VALIDITY OF A SHORT VERSION SCALE FOR MEASURING QUALITY OF LIFE IN RURAL CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The title of this article is ambiguous. Since the authors have addressed that “the purpose of this study is to evaluate the reliability and validity of this scale” in lines 90-91, “studying suicide using proxy-based data” in the title seems unnecessary.
2.	The rationale of conducting this study is not well justified. What benefit or practical significance (such as suicide prevention) could this scale bring to the clinical work or real-world situation? Please illustrate in the Introduction part.
3.	In lines 83-84, the sentence “however, little is known about suicide risks in this rapidly growing vulnerable population” seems irrelevant because this study didn’t investigate the risk factors of suicide.
4.	In line 79, there is format error in the reference “(China, 2019)”.
5.	In lines 99-100, a citation is needed for the sentence “according to the GDP per capita of 31 provinces in mainland China”.
6.	In lines 113-114, does the “average interview time of 90 minutes” refer to a requirement to investigators/interviewers or a calculated average of actual interview time?
7.	In lines 115-117, it would be better understandable if the authors specify which parts of the questionnaires were obtained from the informants and which parts of the questionnaires were obtained from the living controls themselves. Were the sources of demographic information and psychological assessments different?
8.	In line 118, the sentence “the living control was also called the gold standard” was vague. Does the gold standard refer to the information obtained from the living controls themselves or the information obtained from the informants of living controls? Please specify.
9.	In line 132, the international abbreviation for Chinese yuan is CNY, not RMB.
10.	In lines 148-157, the authors should provide all the references of original English versions and validated Chinese versions of all the scales used in this study.
11.	It would be better if the authors could provide the scree plots of exploratory factor analysis.
12.	The full English name of acronyms should be spelled out when the acronym appeared the first time no matter in Abstract or main text part.
13.	In lines 222- 224, how was the sentence “both scores are slightly higher than those in our study” concluded since the total score in Liu’s study is 100 while the total score in this study is 30?
14.	It would be better and more readable if the authors could reorganize Table 1 following the attached format. (I have uploaded an attached PDF containing the suggested format of Table 1)
Experimental design: 1.	The target population in this study is inconsistent. For example, in lines 55-56, the sentence “QOLS-6 … can be used for assessing quality of life among Chinese rural older adults”; in line 86-87, the sentence “however, no studies on the reliability and validity of these scales were conducted in elderly suicide cases”. Is the target population in this study older adults or elderly suicide cases?
Similar situation happened in lines 213-217, the sentence “The scale … provides a useful and practical tool much needed for research on older adults” and the sentence “QOLS-6 has good reliability and validity among Chinese rural elderly suicide cases using proxy-based data”.
Please make the target population and principle study purpose clear throughout the study.
2.	In lines 119-120, please specify the participants from which the informed consent was obtained. The “participants” might differ in suicide case group and living control group.
3.	In lines 163-164, the sentence “ICC is also one of the indicators for measuring and evaluating inter-observer reliability and test-retest reliability” seems unnecessary, because inter-observer reliability and test-retest reliability were not conducted in this study. Inter-observer reliability or inter-rater reliability refers to the degree of agreement among two independent interviewers/raters/trained investigators.
4.	In lines 200-205, the terminologies of “convergent validity” and “discriminant validity” were not appropriate here. Convergent validity can be established if two similar constructs correspond with one another, while discriminant validity applies to two dissimilar constructs that are easily differentiated. Since QOLS-6 and all the other scales used in Table 4 assess different aspects of the target individuals, the authors could consider using the concept of “concurrent validity”, although concurrent validity and convergent validity are both evaluated by correlation coefficient.
5.	In line 231, the terminologies of “external and internal reliability” is not in common use in psychometric studies. The reliability of a scale usually includes internal consistency reliability, test-retest reliability, inter-rater reliability, and parallel-form reliability. Please reorganize the methods and results of reliability accordingly.
Validity of the findings: 1.	In line 160, McNemar’s test rather than Chi-square test, and paired t-test rather than independent sample t-test should be applied because this is a paired sample.
2.	In line 160, the authors declared that Wilcoxon signed-rank test was applied, but the statistics of Wilcoxon signed-rank test are W+ (the sum of positive ranks) and W- (the sum of negative ranks), which were not reported in Table 1.
3.	In Discussion section, the authors should introduce the practical significance of this scale to clinical work, and the methodological limitations of this study.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: STUDYING SUICIDE USING PROXY-BASED DATA: RELIABILITY AND VALIDITY OF A SHORT VERSION SCALE FOR MEASURING QUALITY OF LIFE IN RURAL CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made adequate revisions and reasonable responses according to the previous comments. I have no further comments.
Experimental design: The authors have made adequate revisions and reasonable responses according to the previous comments. I have no further comments.
Validity of the findings: The authors have made adequate revisions and reasonable responses according to the previous comments. I have no further comments.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BIOLOGICALLY-ORIENTED MUD VOLCANO DATABASE: MUDDY_DB
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper describes the establishment of a database that will aid researchers working on the microbiology and geochemistry of mud volcanoes. I applaud the authors for compiling this database. I only have a few suggestions:

- Line 11: In addition to bacteria, these systems also host archaea. I would also suggest to stay general and say that they host various bacteria and archaea after than consortia. Not all live as consortia.

- Line 30/31:  change 'anthropic' to 'anthropogenic' . Also, I would suggest to rephrase the whole sentence as it is not clear what is meant.

- Line 50: I am not sure what is meant by 'biologically flavoured tokens'. Please reconsider rewriting by using different wording.

-Line 59: Again, I am not sure what is meant by 'Token extraction' and 'token' throughout paragraph. Please consider using different wording.

-Line 103: Consider changing to 'one of the settings where life evolved'

- For the web app, I would suggest to make it possible to include a link to the respective papers and data. That will make it easier for people to get the information.

- I understand that the authors were only including only data from open-access articles. However, it would be useful if the authors would include an option to allow investigators to add data from papers that were published in non-open-access articles.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: BIOLOGICALLY-ORIENTED MUD VOLCANO DATABASE: MUDDY_DB
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper described the establishment of a database for mud volcanoes focusing on the biological aspects. Overall, the manuscript is clear and straightforward. However, the authors need to tone down the language in some parts as listed below. Also I suggest the authors to discuss more about why we should care about mud volcanoes. Some detailed suggestions are as follows.

L11 bacterial consortia -> microbial consortia, as both bacteria and archaea can oxidize hydrocarbons.
L13 NLP pipeline -> full name
L17 muddy db is indefinitely available to everyone. -> most likely not all.
L30-31 Pristine oxidation is not influenced by anthropic factors. -> what does this mean?
L28-L31 the authors need to provide more detailed background about MVs.
L36 the authors should explain why NLP is helpful for MV studies.
L45 again, not all the microbiology researchers
L51 had to build -> built
L63 Please also consider GTDB, GENOME TAXONOMY DATABASE; currently more people use GTDB.
L78 vs L58 Please discuss why N is different: 118 vs 115
L79 Rephrase, as it is most likely not indefinitely available for everyone
L99 Please explain DAMO
Experimental design: My main concern on the experimental design part is that the authors need to gather more papers to make the database much more comprehensive. The number of 57 is a rather low number. E.g. L49 I suggest, the authors also explore papers that are also available in fulltext in e.g. researchgate to increase the numbers
Validity of the findings: For this part, I suggest the authors to make DISCUSSION part more meaningful rather than repeat sentences from the introduction and results. E.g. the authors need to discuss both the merits and also the weaking points of the database.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENHANCED SOLUBLE SUGAR CONTENT IN TOMATO FRUIT USING CRISPR/CAS9-MEDIATED SLINVINH1 AND SLVPE5 GENE EDITING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The english needs an improvement. i corrected in the pdf some parts, but I think that should be revised by a native english speaker.
The literature references are appropriate, but I suggest the authors to improve the introduction with a section focused on a brief story on tomato editing approaches, due to the strong application of this technique in this specie.
The reported results are reliable and congruent with the experimental plan. However the discussion about the phenotype development of F2 and wild type, needs to be improved, as marked in the pdf.
Experimental design: The research fits the aims and scope of the journal. The genetic analysis is appropriate, but needs to be improved as reported in the revised pdf (comparison between T0 and F2 values).
Due to numerous application of editing in tomato, the authors should underline, the novelty of this work, that seems to be non so relevant.
The methods are sufficient described, but they could be improved explaining the experimental plan in a detailed way.
Validity of the findings: As previously described, the authors should better underline the novelty of their application, and the validity of the conducted research, respect the others previously conducted.
The data are sufficient, the number of T0 lines is not so high, and the conclusions related to the efficiency of the promoters are not statistic supported.
The final discussion about the phenotypic analysis of F2 and wild type fruits is only qualitative and not metric. Please see the comment in the text
Additional comments: Dear authors, the work needs to be carefully revised and there are some methodological points that are not appropriate developed and supported by quantitative analyses.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENHANCED SOLUBLE SUGAR CONTENT IN TOMATO FRUIT USING CRISPR/CAS9-MEDIATED SLINVINH1 AND SLVPE5 GENE EDITING
Review round: 1
Reviewer: 2

Output:
Basic reporting: English of this manuscript is understandable. However, the English quality is low. This manuscript should be proofread by a professional English proofreader.

I think that sufficient references, field background and context were not provided in this manuscript. Therefore, readers cannot understand background and importance of this study precisely.

Quality and resolution of Figure 1 and Figure 2 are very low.
Experimental design: Aims and scope of this study are clear. However, the presented data and explanations are not enough to tell importance of this study.

Methods was described too roughly and poorly and do not provide sufficient information to be reproducible by another investigator.
Validity of the findings: No comment.
Additional comments: This manuscript entitled “Enhanced soluble sugar content in tomato fruit by CRISPR/Cas9-mediated two genes editing” by Baike Wang et al. reports the production of knock out tomato of two genes (SlINVINH1 and SlVPE5) by CRISPR/Cas9 and increase of glucose, fructose and total soluble solids (TSS) in it fruits. I found high value from both plant physiological and agricultural points of view in this study. However, presented data is not enough to tell the importance of this study and preparation of manuscript is very rough and poor. Comments and requests are written below.

[Major points]

Explanation of experiments and results and discussion of this manuscript is very rough and poor. They should be revised thoroughly. All authors should check again this manuscript and contribute to improve the manuscript.

The mechanism why knockout of SlINVINH1 and SlVPE5 leaded the increase of glucose, fructose and TSS was not discussed. This should be explained clearly and discussed.

Methods was described too roughly and poorly and do not provide sufficient information to be reproducible by another investigator. Methods should be revised.

L288-301 The section “Dynamic variation pattern of the fruit development and coloring”: This is the most critical point. All phenotypic data, including Figure 5, are not quantitative. Quantitative data should be presented. At least data showing fruit size or weight is necessary.

Quality and resolution of Figure 1 and Figure 2 are very low. The figures should be revised. How many genes encoding INVINH and VPE do present in tomato genome? This should be mention in the text. In addition, gene ID for all genes appeared in Figure 1 should be described.

[Minor points]

L32- “In this study, two genes (SlINVINH1 and SlVPE5) that inhibited the accumulation of soluble sugar in tomato fruits were identified” and L347- “The purpose of this study was to identify two tomato genes (SlINVINH1 and SlVPE5)”. SlINVINH1 and SlVPE5 had already been identified as key genes of sugar accumulation in tomato in the previous studies (Jin, Ni & Ruan, 2009; Ruan, Jin & Huang, 2009; Ariizumi et al., 2011; Wang et al., 2016). Therefore, they are not new finding in this study.

L92: Lin 5 is INVINH1. This is written in L116, but it should be mention first appearance.

L97: “maltulose and kestose” should be change to “fructose and glucose”.

L133: “practical basis for the improvement of the flavor of tomato fruits and trait processing”. I don’t understand why this study relate to the improvement of the flavor of tomato fruits.

L206-: “Among the numerous VPE proteins in tomatoes, SlVPE3 and SlVPE5 have been reported to regulate the accumulation of soluble sugars (Ariizumi et al., 2011)”. Why only SlVPE5 was chosen as the target gene of genome editing in this study?

L220-: I don’t understand the meanings of “homozygous mutant”, “biallelic mutant”, “heterozygous mutant” and “chimeric mutants” clearly. Explanation and definition of them are necessary.

L233-239 “In addition, at target-1 site of the SlINVINH1 gene, there are 14 mutations …… the Arabidopsis U6 promoter was higher than that of the tomato U6 promoter” and L326-333 “The sgRNA initiated by the U6 promoter of Arabidopsis thaliana …. sgRNA may also cause differences in the rate of mutation, which is consistent with the findings of previous studies (Ma et al., 2015; Čermák et al., 2017; Shao et al., 2020)”. These descriptions are too speculative and should be removed.

L289: “Because the SlINVINH1 is an invertase gene, loss of invertase function may delay fruit ripening”. This is wrong description. “SlINVINH1 is an invertase inhibitor gene”.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENHANCED SOLUBLE SUGAR CONTENT IN TOMATO FRUIT USING CRISPR/CAS9-MEDIATED SLINVINH1 AND SLVPE5 GENE EDITING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The english sounds professional and clear. The references are correctly provided. The material and methods and the discussion sections are revised and implemented.
Experimental design: The experimental design is more clear and complete. The authors followed the reviewer comments and although the statistical analysis is not so strong, the work is more clear and  inserted in the scientific context
Validity of the findings: The revision addressed the problems of the impact and novelty of the work.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENHANCED SOLUBLE SUGAR CONTENT IN TOMATO FRUIT USING CRISPR/CAS9-MEDIATED SLINVINH1 AND SLVPE5 GENE EDITING
Review round: 2
Reviewer: 2

Output:
Basic reporting: English of this manuscript is understandable. I found several unsuitable/not understandable scientific words. They were pointed out in the following comment.

References, field background and context were added suitably to this manuscript.

Resolution of Figure 1 and Figure 2 are still low.
Experimental design: The manuscript was improved and now the scope of this study became clear.

The methods were improved suitably. Method for measurement of lycopene is missing, thus it should be added.
Validity of the findings: No comment.
Additional comments: I was satisfied with the revised manuscript mostly. However I still have requests and comments as described below.

>>Comment 5: Quality and resolution of Figure 1 and Figure 2 are very low. The figures should be revised. How many genes encoding INVINH and VPE do present in tomato genome? This should be mention in the text. In addition, gene ID for all genes appeared in Figure 1 should be described.
>Respond to this comment: We have made improvement of Figure 1 and Figure 2 to make it more legible.
Reply to the response: Resolution of Figure 1 and Figure 2 are still low.

>>Comment 4: L133: “practical basis for the improvement of the flavor of tomato fruits and trait processing”. I don’t understand why this study relate to the improvement of the flavor of tomato fruits.
>Respond to this comment:The flavor of fruit includes smell and taste, and soluble sugar is the most important component of fruit taste (Mathieu et al., 2009; Tieman et al., 2017). This study increased the amount of soluble sugar in the tomato fruit, so we think this study is related to the improvement of the flavor of tomato fruits.
Reply to the response: As you mention, “flavor” includes smell and taste and soluble sugar is the most important component of taste. In this study, smell of fruit was not checked and smell may not be changed in the genome edited tomato. Therefor “flavor” is not suitable word at least in this sentence and also in other sentences in this text. “taste” or “sweetness” is suitable word in this study.

>>Comment 5: L206-: “Among the numerous VPE proteins in tomatoes, SlVPE3 and SlVPE5 have been reported to regulate the accumulation of soluble sugars (Ariizumi et al., 2011)”. Why only SlVPE5 was chosen as the target gene of genome editing in this study?
>Respond to this comment: It is really true as Reviewer comment that the soluble sugar content was higher in RNA interference lines (RNAi-SlVPE3 and RNAi-SlVPE5) compared with the control plants. However, the soluble sugar content of RNAi-SlVPE5 line was significantly higher than that of RNAi-SlVPE3 line (Ariizumi et al., 2011). Therefore, only SlVPE5 was chosen as the target gene for genome editing in this study.
Reply to the response: Add this explanation in the text.

Additional comments

Why don’t the authors include “SlINVINH1 and SlVPE5” in the title?

 “CRISPR-invinh1” and “CRISPR-vpe5” were used only in Abstract and Conclusion and they are not defined.

L31: “or activating the key protein kinases” is not clear. It had better to be removed.

L88: “Insoluble acid invertase activity decreases significantly in the cell wall” had better to be changed to “The activity of insoluble acid invertase, also called cell wall invertase, decreases significantly”.

L93: “uptake” had better to be changed to “unload”.

L94: “Lin5 influences the biosynthesis of cuticle components. This indicates that the process is coupled with sugar uploading by a mechanism which links the carbon supply with the capacity for fruit expansion  (Vallarino et al., 2017)” is not clear discussion. I suggest to remove these sentences.

Supplementary Table 5 should be moved to the main text with statistical analysis. Table 1 had better to be moved to supplemental data.

L99: The meaning of “pulp” is unclear in this sentence. Use more suitable word.

L118: I sont agree with “The gene SlGLK, which controls the shoulder development of tomato fruits”, because GLK is a master regulator of chlorophyll biosynthesis.

L180: “paper” is wrong. It is “pepper”.

L184-L207: “accession number” other than the first one should be removed.

Quality of the supplementary data is poor. Prepare high quality tables.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ENHANCED SOLUBLE SUGAR CONTENT IN TOMATO FRUIT USING CRISPR/CAS9-MEDIATED SLINVINH1 AND SLVPE5 GENE EDITING
Review round: 3
Reviewer: 1

Output:
Basic reporting: English of this manuscript is understandable.

References, field background and context were added suitably to this manuscript.

Figures and Tables are presented suitably.
Experimental design: The manuscript was improved and the scope of this study became clear.

The methods were improved suitably.
Validity of the findings: No comment.
Additional comments: I respect the work to improve this manuscript by the authors. This manuscript had revised according to my comments and requests properly. I have no more comment or request.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: IDENTIFICATION OF KEYGENES, MIRNAS AND MIRNA-MRNA REGULATORY PATHWAYS FOR CHEMOTHERAPY RESISTANCE IN OVARIAN CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: Good
Experimental design: Author must include construction and analysis of  target genes - TF regulatory network and target genes - miRNA regulatory network along with topology Tables
Validity of the findings: good
Additional comments: Author  must  provided  Differential gene expression (DEGs) table with probe id, logFC, pValue, adj.P.Val, t value and Gene Name, which are more fundamental and basic in this work.
Author must include construction and analysis of  target genes - TF regulatory network and target genes - miRNA regulatory network along with topology Tables