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: THE EFFECT OF MUSIC ON THE PERCEPTION OF OUTDOOR URBAN ENVIRONMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is generally a very clearly written article with a high level of professional English and it gives a good account of the background literature, follows the conventions of experimental reporting, provides clear overviews of all the relevant sections, and stands alone. The data has been shared appropriately.

I just have a few minor presentational points:

In the abstract I wonder whether you could rephrase the sentence about the key findings: ‘only very poorly and nonsignificantly’ could be better framed, perhaps, to say that there is only a slight and not significant influence of music on the evaluation of the environment.

I would suggest using the more precise acoustical terms of loudness or intensity (the latter is used in a few places) rather than ‘volume’ throughout.

A small point: Heye & Lamont (2010) found in their own results that participants often found the music enhanced rather than distracted from their perceptions of their surrounding environment, but this paper is cited in the introduction only in support of the auditory bubble hypothesis of Bull.

There are a few papers in this general area I am aware of which were not cited and the authors may wish to consider whether these are relevant: since there has been so little published on this specific topic, it might be useful to include these, and to take a further look at whether there are other relevant studies in this broader context.

Riener, C.R., Stefanucci, J. K., Profitt, D. R., & Clore, G. (2011). An effect of mood on the perception of geographical slant. Cognition and Emotion, 25(1), 174-182 (shows that manipulating mood through different types of music affects perception of slant in hill)
Bhattacharya, J., & Lindsen, J. P. (2016). Music for a brighter world: Brightness judgment bias by musical emotion. PLOS One, doi.org/10.1371/journal.pone.0148959. (experimental manipulation through music, happy music led to brighter, sad music led to darker perceptions of a grey square)
Ehret, S., Schroeder, C., Bernet, J., Holzmüller, & Thomaschke, R. (2019). All or nothing: The interaction of musical and spatial atmosphere, Psychology of Music, doi:10.1177/0305735619880288 (also experimentally investigates the effects of valence in music and spatial atmosphere in more controlled conditions).

Methods: line 214 should be ‘ninety-four’ not ‘nine-four’.

I would reframe the way the music stimuli are described as rather than being ‘borrowed’ from an earlier study they simply are used from it – and this is extremely good practice in the field, so should be celebrated (the use of ‘borrowed’ sounds a little apologetic). I wonder whether it would be better to label the types of music as ‘motivational’ and ‘non-motivational’ throughout, rather than the shorthand of ‘fast’ and ‘slow’ (e.g. line 235) or the variable names of Music1 and Music2 (which the reader doesn’t necessarily remember throughout – this is used in the figures). I think it would also be useful to emphasise here, given the importance of liking later on, that this music was chosen to be liked by the participants, and to remind the reader of this in the liking section of the results.
Experimental design: The study includes a well defined research question and a highly appropriate range of experimental variables (type of music – fast/slow; type of environment – urban build/urban natural; outcome measures (emotional and spatio-cognitive dimensions), with control applied to the intensity dimension to make the music only background.

It would be helpful perhaps to show some photographs of the environments used, which might help in relation to the comparison with the previous study and also to elaborate what ‘openness’ means (lines 283/4) as this was not entirely clear. If not, then a fuller verbal description might be useful, particularly in Table 2.

The ratings are quite brief (single questions per dimension) compared to the Yamasaki et al. study, and while this was obviously helpful from a practical level I would like to see some evaluation of the effects this might have had on responses.
Validity of the findings: Overall the results are reported appropriately and the findings are generally clear, with appropriate interpretations drawn (with one exception noted below about music experience/training).

Liking for the music is mentioned in the results but there could be more discussion about liking for the environments. Presumably, given the importance of the emotional responses to the environmental variables, this will also play a role, and even though explicit data was not gathered, there could be some speculation about this effect (the pleasantness dimension might be something to pull out even more). The assumption is that the music influences the environment but it is also possible that the relationship goes the other way, which I think is what was intended by the analysis of music liking as a mediator and this point could be brought out more explicitly.

In terms of speculation, the points about musical experience in the Discussion should, in my view, be toned down and reframed somewhat. I would like to see ‘musicians’ reworded as ‘musically trained adults’ because arguably everyone is a musician. More substantially, there is some speculation here about the musical backgrounds of participants without appropriate support from any systematically gathered data and I think the point made ought to be toned down to suggest that music training is a variable to be included in future investigations. I would also suggest that this could be broadened out to include a measurement of active engagement with music, such as the Goldsmiths Musical Sophistication Index Active Engagement scores which provide information about the amount of music listened to, interest in music listening and so on which might help explain individual differences in results.
Additional comments: Overall this strong paper contributes to a small but important field, of relevance to the journal, and taking account of the above relatively minor comments this would make a valuable addition to the 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: THE EFFECT OF MUSIC ON THE PERCEPTION OF OUTDOOR URBAN ENVIRONMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. This study examined whether background music can modify the impression of a visual environment. The article is written in clear English.
Experimental design: The experimental design is good.
Validity of the findings: No 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: THE EFFECT OF MUSIC ON THE PERCEPTION OF OUTDOOR URBAN ENVIRONMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: I think that this article is written by professional English in general. All sentences are clear and unambiguous. But, there are small typos between “,” and “.” in p-values in line 396 and 399.

The references cited in the introduction are adequate and new. However, the list of references should be corrected because the order, especially from the initial “k” to “l”, is confused.
Experimental design: Research question is clear and within the scope of the journal.

In this experiment, the characteristics of musical materials are very important. Although authors focus on the motivational characteristics of music listened to, the musical characteristics which affect the evaluation of given environments are not limited to it. Therefore, more detailed descriptions of the musical materials are desirable, such as semantic profile of the musical materials by SD method. If it is confirmed that Music 1 and Music 2 differed extensively in many aspects of those perceived characteristics, authors’ conclusion, the poor influence of music on the evaluation of environments, will be more persuasive.
Validity of the findings: It is really important findings that the liking of music and the disturbance of music mediate the effect of music. But, according to the descriptions, authors drew this conclusion from ANOVAs in which the liking score was dependent variable with five levels. If so, multiple comparison tests are necessary for the investigation of the direction of effects of music liking. About the disturbance of music, the same can be said.

In this study, participants heard music at lower level than a previous study by Yamasaki et al. (2015). They heard music not only at each selected environment, but also during moving between environments. Authors consider these experimental conditions as more realistic than Yamasaki et al.. Indeed, continuing to hear music during moving may be closer to the everyday music listening situation of participants. However, because listeners with portable music players in outdoor settings decide to do it by themselves, their attitude to listening may be more intentional and their volume of music will be not so low. In addition, it seems to be less realistic that participants hear only a song during a lasting event. Thus, some features of the experimental conditions which authors set up seem to be closer to ones of in-store settings with background music rather than ones of personal use of music in outdoor settings. This doesn’t reduce the value of findings in this study, but influences the theoretical and the practical meanings of findings. Therefore, more discussion on this topic is desirable.
Additional comments: I believe that the present study is worth publishing. I hope that my suggestions are helpful to your work.

In order to understand the results of this experiment, it is very helpful for readers to grasp the experimental stimuli clearly. Music stimuli can be listened to easily from Youtube etc., while visual environments are difficult to be seen. So, pictures will be very helpful, if possible.


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 A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, the authors determined a list of patient prognosis predicting differentially expressed metabolism-related genes (MRGs) signature by analysing RNA sequencing data of hepatocellular carcinoma (HCC) samples in The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. They also determined that the identified genes signature has association with sorafenib responsiveness; and also has prognostic value for HCC patients who are male, ≤65 years old, and wild-type for TP53 and CTNNB1 genes.

The manuscript was written using clear professional English. However, sufficient background/context with literature references was not provided in the manuscript. For example, the background information and reasoning for why the authors aimed to focus on analysing the differential expression of MRGs to generate a prognostic model for HCC should have been clearly explained. However, the authors provided only one sentence without a reference. In addition, references of some of the background information were not presented; such as sentences in lines 61-62 and 64-66. Furthermore, the mutations of TP53 and CTNNB1 genes were defined as the major cancer drives for HCC in the manuscript. However the genetic etiology of HCC is more complex and cannot be explained with mutations of two genes. Therefore the reasoning for focusing on mutations of TP53 and CTNNB1 genes in the study should be peformed by providing a more approriate background information, as well.
Experimental design: The following major issues about the experimental design of the study have been determined:

•	The method for generation of the list of MRGs were described in the manuscript with only one sentence as “MRGs were extracted from the file “c2.cp.kegg.v7.0.symbols.gmt” in the gene set enrichment analysis (GSEA) database.” The list generation method was described with insufficient information to replicate. Because,
i.	the total number or the list of MRGs were not presented,
ii.	“c2.cp.kegg.v7.0.symbols.gmt” file contains 186 different genesets. There are lots of genesets, which are irrelevant to metabolism, in this gmt file, such as KEGG_OOCYTE_MEIOSIS, KEGG_CARDIAC_MUSCLE_CONTRACTION, KEGG_AXON_GUIDANCE, etc. Whether these genesets were discarded or included in the study was not explained in the manuscript.

•	GSEAs were performed using data of 343 HCC samples from TCGA database and 230 samples from ICGC database, using the same genesets list, which was used to generate the MRGs list (c2.cp.kegg.v7.0.symbols.gmt). However, the initial number of HCC samples analysed from TCGA and ICGC databases were 374 and 243, respectively. The reason of this difference was not described. In addition, it would be better to perform GSEAs by using the complete c5 and c2.cp genesets lists, since these lists include genesets from additional pathway and ontology databases, such as Gene Ontology and Biocarta. This approach might significantly improve the experimental design of the study, because it is stated in the manuscript that “Further, we were unable to discover the underlying mechanisms of some of the genes in the signature”, and analysing additional databases may provide valuable mechanistic data from a different source.

•	The authors, without providing a reference, stated that “The tumor suppressor gene, TP53, and the oncogene, CTNNB1, are the two most commonly mutated genes in HCC and are associated with poor prognosis.” Although TP53 and CTNNB1 genes are the two most frequently mutated genes (31% and 27%, respectively), according to exome sequencing data of HCC samples in TCGA database there are also other known frequently mutated genes, such as NCOR1 (22%), RB1 (19%), and ALB (13%) (1). Therefore, either all known frequently mutated genes should be analysed and reported in the study or the satatement should be revised in the manuscript to provide an unbiased reason for focusing on TP53 and CTNNB1 mutations to reveal an association between MRG signature and OS in HCC patients.

References
1. Cancer Genome Atlas Research Network et al. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell, 2017. 169(7):1327-1341.e23.
Validity of the findings: The following major issues about the experimental design of the study have been determined:

•	Since all analyses were performed after determining the list of MRGs, the previously mentioned problems about the experimental design of the study effect all results and limit the validity of all the associated and following findings.

•	All the differentially expressed MRGs lists, namely the 54 differentially expressed MRGs list, 22 differentially expressed overall survival-related genes list, and the nine MRGs list, which was used to build the prognostic model for HCC, contain genes with very low mean expression values (as seen in figure 1E and Table 1S). Although fold change values of these genes are high and p values are statistically significant, very low expression values of these genes suggest that molecules encoded from these genes may not be crucial for metabolic functions of both normal liver and HCC cells. Therefore a cut off value should be determined for identification of differentially expressed MRGs. As a result, the validities of all the following findings that rely on MRGs list are limited, because the results were obtained based on very-lowly exppressed MRGs inluding genes list.
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: IDENTIFICATION OF A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Tang et al. described a prognostic gene signature for HCC, which is composed of nine metabolism related genes. The gene signature is validated in an independent dataset and seems to have some predictive power in terms of overall survival in male patients <65 years of age and patients carrying the wild-type TP53 or CTNNB1 genes. The manuscript is written in clear and technically correct English. My only criticism here is for line 269-270; `..Auranofin, a TXNRD1 inhibitor, effectively clears this stress and sensitizes HCC cells to conventional sorafenib therapy..`
The TXNRD inhibitor shall exacerbate oxidative stress, rather than clearing it to sensitize HCC cells to sorafenib therapy.
Article figures are relevant to the content of the article, appropriately described and labelled.
Experimental design: Aim of the research is to define a metabolism associated molecular signature to stratify HCC patients into high and low risk sub-groups. However, the literature in the field is not short on prognostic gene/miRNA signatures; in the case of HCC, dozens of prognostic gene signatures have already been reported. Therefore the novelty of the current gene signature is not inherently clear, especially considering that it does not predict something directly actionable (e.g. likelihood of recurrence, metastasis, sorafenib responsiveness  etc.). Comparative analysis depicting the relative efficacy of this prognostic signature over others could add potential novelty to the study.
Methods are described with sufficient detail and information.
Validity of the findings: In general, validity of the findings are rigorously tested in the manuscript. All underlying data have been provided; they are robust, statistically sound and controlled. One major criticism here though is the use of overall survival as the only clinical parameter to establish validity of the gene signature in ICGC cohort. HCC differs from most cancers in that there are two biological processes to simultaneously consider. It usually arises within a liver compromised by cirrhosis, thereby requiring effective management of two disease processes. Thus, death from disease progression may arise from distinctly different causes – recurrence and/or dissemination of the HCC, de novo new HCC arising in the cirrhotic liver, and complications of progressive cirrhosis including hepatic decompensation. Thus inclusion of disease free survival into the pipeline can in principle combine all three processes noted above – recurrence and/or dissemination of HCC, de novo new HCC arising in the cirrhotic liver, and complications of progressive cirrhosis.
As a minor point, I found it a little farfetched  to consider genes depicted in the signature as potential targets of sorafenib.The involvement of the majority of these genes in the pathophysiology of HCC has not been firmly established.
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: IDENTIFICATION OF A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is poorly written, need a clearer description of the analysis. Additional editing would help make the paper easier to read and interpret.
Experimental design: The choice of data sets is not well explained – given that these are the starting point for all of the analysis this is an oversight that is not acceptable. HCC samples descriptions should be done such as which type of cells or tissues were selected for analysis.
Systems biology and bioinformatics related studies differ from each other in terms of used algorithms. But, in this paper, there is no special algorithm or method to identify nine prognostic genes. As far as I understand, 9 prognostic genes were selected from common deg. But it is acceptable but makes the method weak.
Identification of Sorafenib response to the nine gene expression profiles is a good idea but prognostic potential should be investigated via Kaplan Meier plots. Moreover, AUC values (Fig 2)  are not very good, compared with other study results. It must be discussed what is good.
In fig 1, different gene expression profiles obtained from the TCGA and ICGC cohort have seen in the heat map. Please discuss why direction of gene expressions is different? The prognostic analysis is performed based on gene expression therefore the direction of gene expression (up and down-regulation) is crucial.
Why selected only two genes (CTNNB1 and TP53)? Are there other genes that show a higher mutation in this cancer? The authors make sure there are genes with the highest mutation?
Validity of the findings: This study represent novel results in terms of nine prognostic genes. I can't be sure that novelties of the genes for HCC prognosis. Unfortunately, these genes whether or not they are novel for HCC is not discussed. So, in the discussion part, nine genes related to HCC studies should be summarized as a table. The prognostic and diagnostic potentials should also be investigated from literature.
Additional comments: The paper utilizes existing gene expression data sets for HCC from two databases. Differentially expressed genes were identified and common 9 prognostic genes were found.  And then further analysis are about the validation of the prognostic potential of nine genes in HCC. Unfortunately, the idea is not interesting, there are similar lots of studies.
Some of them: Comprehensive analysis of potential prognostic genes for the construction of a competing endogenous RNA regulatory network in hepatocellular carcinoma
C Yue, Y Ren, H Ge, C Liang, Y Xu, G Li… - OncoTargets and …, 2019 -

Development and validation of a three-gene prognostic signature for patients with hepatocellular carcinoma
B Li, W Feng, O Luo, T Xu, Y Cao, H Wu, D Yu… - Scientific reports, 2017 -

Systems biology and bioinformatics related studies differ from each other in terms of used algorithms. But, in this paper, there is no special algorithm or method to identify nine prognostic genes. As far as I understand, 9 prognostic genes were selected from common deg.


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 A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made appropriate and acceptable changes regarding the requested revisions.
Experimental design: The authors have made appropriate and acceptable changes regarding the requested revisions.
Validity of the findings: The authors have made appropriate and acceptable changes regarding the requested revisions.
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: IDENTIFICATION OF A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors did a fine job in improving the clarity of the text. Literature is appropriately cited; more detailed background is given according to the reviewers suggestions.
Experimental design: The revised manuscript is more explicit in describing the experimental methodology.
Validity of the findings: In general, the revised manuscript reads better with the inclusion of discussion points that add further relevance to the in silico findings. One potential controversy which may need addressing is the following;
Authors indicated that changes in metabolic pathways that are driven by oncogenes, are recognized as cancer markers; and indicated TP53 and CTNNB1 as such genes suggesting a probable route for metabolic reprogramming. Although the authors utilized a strictly metabolic gene signature, how come that signature only has predictive power in TP53 and CTNNB1 wild type patients? Would it not make more sense for such a metabolism driven signature to be a better prognostic factor in TP53 and CTNNB1 mutant HCC, where cellular metabolism is shaped by the mutant oncogene?
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: IDENTIFICATION OF A PROGNOSTIC SIGNATURE OF NINE METABOLISM-RELATED GENES FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 3

Output:
Basic reporting: Literature references, sufficient field background/context provided.
Experimental design: It is suitable.
Validity of the findings: It is suitable
Additional comments: This paper is suitable for publication.


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, this is a well written and well organized manuscript, but some corrections and observations indicated in the text of the attached file must be attended.
Experimental design: This manuscript examine the R2R3 MYB transcription factor in two species of ornamental orchids of economic importance, and also investigate the expression in different tissues, and the effect of some abiotic stresses (salinity and drought) on the expression of them. This kind of analysis has not been explored previously in these species. The analysis of the R2R3 MYB transcription factors was well performed, and also were the expression analyses. Methods were well described and should allow to replicate them.
Validity of the findings: All underlying data have been provided. They are robust, statistically sound and controlled.
Conclusions are well stated.
Additional comments: Authors should prepare the corrected manuscript following very carefully the Instructions to Authors Guide.


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, the authors analyzed sequenced genomes of two Orchid species and identified 101 and 99 R2R3-MYB genes from Dendrobium officinale and Phalaenopsis aphrodite, respectively. After a series of bioinformatics analysis, they further classified them into 22 subfamilies based on a homologous analysis against AtR2R3-MYB genes. Using qRT-PCR, the expression patterns of six subfamily members of the DoR2R3-MYB genes in different tissues were analyzed and the results revealed that the S4 and S19 subfamily members had the highest gene expression levels in flowers. In addition, expression levels of a few DoR2R3-MYBs in response to salt, osmostic, ABA, JA etc treatments were assayed. Though these results presented may provide useful information for further studies of the R2R3-MYB gene family in the two orchid species, overall, the data were quite preliminary and very descriptive, which lack further confirmation or investigation.
Experimental design: obvious drawbacks exist with some experiments
Validity of the findings: limited
Additional comments: In this study, the authors analyzed sequenced genomes of two Orchid species and identified 101 and 99 R2R3-MYB genes from Dendrobium officinale and Phalaenopsis aphrodite, respectively. After a series of bioinformatics analysis, they further classified them into 22 subfamilies based on a homologous analysis against AtR2R3-MYB genes. Using qRT-PCR, the expression patterns of six subfamily members of the DoR2R3-MYB genes in different tissues were analyzed and the results revealed that the S4 and S19 subfamily members had the highest gene expression levels in flowers. In addition, expression levels of a few DoR2R3-MYBs in response to salt, osmostic, ABA, JA etc treatments were assayed. Though these results presented may provide useful information for further studies of the R2R3-MYB gene family in the two orchid species, overall, the data were quite preliminary and very descriptive, which lack further confirmation or investigation.

There are quite some evident grammatical errors or typos, which need to be intensively examined and corrected. To list just a few:
Lines 14-15: some words are missing in this sentence.
Line 18: delete the last “the”
Lines 59-61: several errors, need revision

Line 19: not clear what the authors wanted to say by “most of proteins were DNA binding proteins”. Are there any R2R3-MYB proteins that do not bind DNA at all (similar to members of bHLH family)?

Lines 72-88: what did the authors do to differentiate the R2R3-MYB TFs from others? The algorithm used to construct the tree should be clearly stated here.

Lines 133-139: why were the duration of treatments of salt, mannitol and ABA longer than other hormones? What is the reason or rational? Usually for transcriptional profilings, better to limit treatment duration to hours (e.g. max 2 d).

For qRT-PCR assay of tissue specificity, how were expression levels compared to? From the data presented in Fig 6, it can be seen that the expression levels in roots were arbitrarily set as 1.

For Fig 7, beside time 0 h control, how did the authors calculate the ratios? This kind of into should be stated clearly in both figure legends and materials and methods.

Line 142: What is the database acc# of reference gene β-Actin? Why was it used as a reference gene? Is there any evidence that this gene is stably expressed under various stress conditions or in different tissues and organs? Usually, at least two different and stable reference genes should be used with geometric means calculated. Leave a space between numerals and units.

In the Discussion section, result figures should be referred to at appropriate sites.

Fig. 1: the font of bootstrapping percentages is too small to be seen.

Fig 2: very obscure, font of text is too small

Fig. 4: the gene symbols are not right

Fig 6: legend is not complete or self-explanatory. The SDs are very tiny indicating no biological replicates were done. Any qRT-PCR data with only technical replicates are not acceptable. The same problem occurs to data presented in Figs 7&8.

Statistical analysis is missing in either Fig 7 or 8. Without it, it is not scientific to say if a change is significant from mock treatment or not.


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article must be written in better English. any mistakes in English style and grammar can be found throughout the manuscript. There are many typos and some inaccuracies that should be corrected.

The “introduction” did not provide sufficient background, thus it needs more literature highlighting this topic, and more bibliography should be included. The ms should include more sufficient intronduction and background as well.
Experimental design: The “material and method” section is not clearly nor concisely written, and at the same time lacks of many essential details.
Validity of the findings: The results and conclusions should be more well stated. Most of the results are not explained and presented well. Many parts are descriptive and lacks of scientific soundness, and should be extended to unravel the story in detail.
Additional comments: MYB proteins have interested biologists for a long time and their roles have been deciphered in a number of organisms. The manuscript by Fan et al. reports a genome-wide anlaysis of the R2R3-MYB family in two Orchid species, Dendrobium officinale and Phalaenopsis aphrodite. First, the authors identified R2R3-MYB coding-genes in these two species. The work continues with a phylogenetic and genomic analysis (chromosomal distribution, gene and protein structure analysis), followed by a global expression profile analysis for different tissues at different developmental stages, as well as in response to stress treatments. Furthermore, the authors studied by qRT-PCR the steady-state levels of transcripts of 20 representative genes in response to salt stresses. This work is basically bioinformatics, which is fundamental for a genome-wide analysis of gene families. Although the experimental strategy in this manuscript is appropriate, the study is very descriptive and lacks of scientific soundness. The authors have drawn hasty conclusions. Many mistakes in English style and grammar can be found throughout the manuscript. There are many typos and some inaccuracies that should be corrected. Turning it very difficult for the reviewer to evaluate their scientific significance.
Additional comments follows.
1. Line 12, replace “plant growth and development” with “plant growth, development and stress response”.
2. line 14-15, it is a bad sentence. You must re-write it.
3. Line 17-18, bad sentence. It is hard to under your mean of “There were different numbers of introns, exons and conserved sequences in all of the identified genes”. The statement is unclear and very confusion.
4. Line 18, “They” indicate what? Intron, exons and conserved sequences? If yes, how intron “evolved at the protein level”? And the statement of “conserved sequences” is very confusing.
5. Line 20, you just performed the chromosomal distribution analysis of PaMYBs? How about the BoMYBs, as the title and main contents of this ms are about the R2R3-MYB genes in these two species. Similar problems are existed in the whole text. Thus this paper is disordered in many parts, and the authors should state your idea and results more clearly to avoid confusion. The authors should check logic in the whole text.
6. Abbreviation, such as PaMYBs and BoMYBs in line 20 and 23, should be defined at the first time in Abstract, Figure legend, and main text respectively. Moreover, PaMYBs and BoMYBs may be replaced with Pa2R-MYBs and Bo2R-MYBs to distinguished from thr other types of MYB super family (1R-MYB, 3R-MYB, and 4R-MYB).
7. Line 22, “further quantitative analysis to determine their function” is not rigorous, because it is hard to determine gene function merely by quantitative analysis.
8. Line 23, delete “As a result”.
9. Line 24, “Parts of” is obscure. And, as mentioned above, why do you choose to analyze the expressions of BoMYBs in stead of PaMYBs?
10. Line 27, replace “Bioinformatics” with other key word(s) related to this study.
11. The “introduction” did not provide sufficient background, thus it needs more literature highlighting this topic, and more bibliography should be included. For example, first paragraph in this section, the major functions of R2R3-MYB genes are involved in metabolism, growth/development, and stress.
12. Line 44, the size of “Rabinowicz” is different from the main text?
13. For the logic issue, the second paragraph in this section should be the first; the first and the third paragraphs are somewhat overlaped.
14. Line 50-51, rewrite this sentence.
15. Line 56, “Arabidopsis thaliana” should be “A. thaliana”. Similar problems should be corrected in the whole text.
16. Line 64, repace “in all aspects” with “in many/diverse aspects”.
17. The “material and method” section is not clearly nor concisely written, and at the same time lacks of many essential details. For example, line 82, it is dangerous to delete the redundant MYB sequences based on sequence alignment, as some recently duplicated genes may have high sequence identity (even the same). Line 85, it is inconceivable to use the MEGA5.2 software with default parameters to construct the phylogenetic tree. What is the detail information of “default parameters”?
18. Line 87, replace “Arabidopsis thaliana” with “A. thaliana”.
19. Line 104, “MeGA 5.0” should be “MEGA 5.0”?
20. Line 111, “PaR2R3-MYB” should be unified in the whole text.
21. Line 117, should state why just analyze the expression profiles of MYB genes in D. officinale.
22. Line 122, the raw data was normalized or log2-transformed before making heatmap?
23. Line 123, why do you choose the 20 DoR2R3-MYB genes to do co-expression analysis? And the co-expression analyses should be performed at the genome-wide level, in stead of just the 20 genes.
24. Line 130, why use “a tissue culture seedling”?
25. Line 142, supply the GenBank ID of β-Actin gene.
26. Line 144-145, re-write this sentence.
27. “Results” section, most of the results are not explained and presented well. Many parts are descriptive and lacks of scientific soundness, which include a lot of contents about the corresponding methods. The authors should focus on the scientific issues. Many sections should be extended to unravel the story in detail. Figures 1-5 should be explained further to unravel their significant findings.
28. Line 156, why S6, S12, and S15 did not have members in these two species investigated? The information about the results in this part is too simple. The distribution situation of the candidate genes in the same subfamily between the two species is the same?
29. Line 166-168, in fact, there are many literatures have proved that the intron patterns in the MYB domains of 2R-MYB genes were generally conserved in many subfamilies. The analyses and results in this part are too obscure.
30. Line 202, “99 Pa R2R3-MYB genes” should be “99 PaR2R3-MYB genes”? “85  genes were mapped”, how about the remainings? Moreover, how about the situation of BoR2R3-MYB genes?
31. Line 207, how did you identified the “33 pairs” genes?
32. Line 209, what’s the method that was used to identify the segmental duplication?
33. Line 213, the statement of “almost identical (> 80%)” is not rigorous.
34. Line 214, why did you just focus on DoMYB? How about the PaMYB genes?
35. Line 219-223, what’s the main result about the 65 genes? Here, you just focus on the results of a few genes (18 genes), why?
36. Line 224-234, How about the results between the RNA-Seq and qRT-PCR analyses.
37. Line 237, replace “under stresses” with “under drought stresses”.
38. Line 249-258, given the homologs may have similar expression patterns, thus the co-expression analysis of them is meaningless. It is better to perform this assay at a genome-wide level to speculate the co-expression network of them.
39. In the qRT-PCR expression analyses, statistical analysis should be clarified and the softwares used should be mentioned in details. The statistical analyses performed to find significant differences are not shown in Figure 6, 7 and 8.
40. Figure 1: Increase the size of the letters. It is difficult to see the names of the genes and the bootstrap value on the phylogenetic tree. Moreover, the legend of the picture should be more clarified, and the “Dendrobium officinale”, “Phalaenopsis aphrodite” and “Arabidopsis thaliana” should be in italic.
41. Figure 2: Increase the size of the letters. It is difficult to see the names of the genes the illustration, and the lables in the picture. Figure 2C is hard to read, and should be great imprvoed.
42. Figure 3: Why the number of amino acid in A & C, and B & D are different?  Increase the size of the letters.
43. Figure 4: Increase the size of the letters. It is difficult to see the names of the genes the illustration, and the lables in the picture.
44. Figure 5. The size of the letters should be increased. The gene names are different from these in the text? The figure represent log2 expression values (FPKM>1)?.
45. Figure 6, 7 and 8 should be replaced with high resolution figures.
46. The discussion still needs improvement and explanation in detail. The discussion should show how these new findings in this study support the research question and hypothesis.


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have a look at the revised manuscript, and found out that though the authors have solved most of my concerns or questions, there are still a few waiting to be solved or touched up.
For example, the title is not right, add “genes” after “factor”, since only DNA or RNA sequences were surveyed and analyzed in this manuscript. No protein work has been done at all.
Abstract, line 21, several typos or errors are identified.
Line 23: stresses->stress
Line 26: were responsible for->responded to
Still, a few grammatical errors or errors still exist in the whole text including legends.

Figs 7&8 are still obscure with too small font size, the same with the two in the Word file of responses to reviewing comments. The authors should understand that under 100% view, all figures or tables should be recognized and readable (though some figures in some other journals are also very hard to read still; I dislike those very much). At least a higher resolution figure should be provided in the supplemental data.
It is not acceptable to set up only three technical replicates for qRT-PCR assays (and many other assays, if there are). This mean that sample preparation, RNA extraction, removal of contaminated genomics DNA, RT and follow-up qPCR should be repeated three time independently, to constitute three biological replicates. Many other papers published in many journals did not abide by this simple rule either and I doubt their conclusions and relevant data.
Experimental design: see the above text
Validity of the findings: see the above text
Additional comments: see the above text


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: There still are a lot of problems in the full text (even some serious problems), and some of my last comments are not well addressed.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Comments to the Author (s):

As mentioned in my last comments, there were many problems in the manuscript, especailly some serious problems. Some of my last recommendations have been addressed by the authors, but some problems have not been well addressed, and there still are many problems in the full text. In fact, the authors focus on answering/explaining my comments point by point, instead of paying attention to the corresponding scientific issues and doing some revision in the text. Some major points listed below does not convince me that it meets the general criterion for publication in this journal.

Major comments:
1. There are a lot of format error in the whole text, even in the “Abstract” (such as line 15, 21, etc). And there are many blank spaces and lines in the text, such as line 41, 111, 178-179, etc. The authors are very careless.

2. Last time, I have suggested that “Many mistakes in English style and grammar can be found throughout the manuscript. There are many typos and some inaccuracies that should be corrected”. The writing needs to be thoroughly checked and substantially improved by English language editing company.

3. The authors defined “DoR2R3-MYB” and “PaR2R3-MYB” in “Abstract” to distinguished them from the other types of MYB super family (1R-MYB, 3R-MYB, and 4R-MYB). However, the gene names are still BoMYBxx (such as line 26 in “Abstract”). As we know, the R2R3-MYB genes are commonly named as MYB gene. If the authors want to keep this nomenclature, it is better to define it more clearly to avoid confuse, and unify the style in the whole text.

4. Last time, I have suggested that “it is inconceivable to use the MEGA5.2 software with default parameters to construct the phylogenetic tree. What is the detail information of default parameters?”. However, the authors did not understand my mean. For the phylogenetic analysis by MEGA software, the important parameters include “Tet of Phylogeny”, “Model/Method”, and “Gaps/Missing data treatment” which may impact the results directly, thus, should be clearly stated. Moreover, the NJ tree was constructed based on the full length or only the BD domains of candidate protens? It is unclear too.

5. For the “Intron-exon structure and domain analysis of R2R3-MYB genes from D. officinale and P. aphrodite” section in line 95-99, the authors should clearly state the sequences that were used in these two analyses. As we know, the MYB TFs are generally consisted of a N-terminal BD domain and a C-terminal AD domain. The BD domain is highly conserved across this gene family, thus the intron pattern is generally conserved in this region while it is not conserved in the AD region. For the MEME analysis, it is better to use the AD region, as the BD domain is actually conserved.

6. Line 132, the authors still did not state why and how they seleted the 20 genes for qRT-PCR analysis. The authors should let the potential readers know it, instead of just explain to me.

7. The method used to identify the segmental duplication was wrong, thus the corresponding results are incredible. You should note that all duplicated genes may share high sequence identity including tandem duplicaion, segmental duplicaion and so on. So, it should be identified on the basis of collinearity analysis, instead of just the sequence similarity.

8. There is even an erasure mark in Figure 1? It is bad.

9. The explain for my last comments about Figure 3 is unconvincing. Yes, the sequences between two species or even two proteins might be different, but the length of the BD domain (R2 and R3 repeats) is commonly conserved. There are a lot of published papers have proved this characteristics.

10. As you stated that you mainly focus on the MYBs in Dendrobium officinale, so the chromosomal distribution information of the MYBs in Phalaenopsis Aphrodite in line 217-229 should be deleted or moved to Supplemental data. Beacuase the chromosomal distribution of this gene family in these two species are different, it can not represent the situation in D.officinale.
11. last time, I asked the authors that “Line 219-223, what’s the main result about the 65 genes? Here, you just focus on the results of a few genes (18 genes), why?”. And the authors response to me that they just want to analyze the tissue-specific expression pattern of all 101 DoMYB genes using the transcirptome data. However, line 237-238, they wrote that “8 genes were expressed in all seven parts.” It is obvious that these genes are not tissue-specific. Accordingly, the explain for this issue is incredible. It is still hard to understand why they just anlayzed the expression profiles of the 18 MYB genes, instead of the 65 genes that have detectable transcriptome in the RNA-Seq dataset investigated.


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 3
Reviewer: 1

Output:
Basic reporting: This is a revised and corrected manuscript dealing with the analysis of MYB transcription factors in two orchid species: D. officinale and P. aphrodite. In this version the authors attended the corrections, comments and observations made previously by the reviewers. English language used throughout is clear and professional now. Literature references were prepared according to the Instructions for Authors guide and are sufficient. This article was prepared properly with professional structure, figures, tables and suppemental material, and contained relevant results linked to the hypothesis.
Experimental design: Original primary research within Aims and Scope of the journal.
The research question was well defined, relevant for people in the orchids area and stated how the research fills knowledge gap.
Rigorous research performed properly with ethical standard.
Methods were described clearly and with sufficient detail to be replicated.
Validity of the findings: The findings are novel and original and contribute to the knowledge of the MYB family in orchids.
All underlying data have bee provided; they are robust, statistically sound and controlled.
Conclusions were well stated, linked to original research question.
Additional comments: No furtehr 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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 3
Reviewer: 2

Output:
Basic reporting: I had a look at the revised manuscript again and found that the authors have solved almost all my previous concerns. Thus, I’d recommend an acceptance of it provided that the authors correct the follow tiny errors:

Fig 4 legend: based->based on
Fig 5 legend: qRT-PCR validation of R2R3-MYB transcription factors-> qRT-PCR validation of R2R3-MYB transcription factor genes; The average data was-> The average data were
Figs 4&5: gene names should be spelled in italics
I’d suggest that authors check the whole text again carefully to minimize or avoid the above kinds of errors as I do not have time to point them out one-by-one.
Experimental design: no further comments
Validity of the findings: no further comments
Additional comments: no


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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSES OF R2R3-MYB TRANSCRIPTION FACTOR GENES FROM TWO ORCHID SPECIES
Review round: 3
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Comments to the Author (s):

All of my last recommendations have been well addressed. I think that this new revision can be accepted for publication now. But, there are stilll several minor problems should be addressed before it is publicated.

Hai Du

Minor comments:
1.	Althought the English language of the ms has been greatly improved in the last revision by the authors, there still are some language problems in the text (such as “subfamily” in line 24 in “Abstract” should be subfamlies). So, the writing needs to be thoroughly improved by a language company.
2.	To avoid confusion, the gene names in Figure 5 should be changed into “BoMYBxx”.
3.	In my opinion, the letters A-T in Figure 6 and 7, and their related contents in the figure legends are not necessay, as the gene names have been marked in the figures.


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 RISK FACTORS FOR MORTALITY ASSOCIATED WITH COVID-19
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally well written, but needs to avoid repetition (e.g., The sentence, “The mortality rate was 17.1%”, repeated several times). It provided enough background, literature reviewing, and references. The manuscript is well organized and easy to follow. Figures and tables are all in the right format. In the manuscript, it is claimed: “the datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request”. However, the paper does not have a significant contribution in theory; the major contribution of this paper is on the application side, which is heavily relying on the data. I am not quite sure if the availability of data is conditional, will it influence the acceptance of the paper?
Experimental design: This is an original primary research within the scope of the journal. The research question is well defined and meaningful. The statistic results and the established predictors may provide valuable tools for the identification of vital status at the hospital discharge about COVID19. The technical and ethical standards of the paper are high. It also provided enough details about experimental setting and data collection.
Validity of the findings: The benefit of the research is significant as it directly addresses some critical issues of the COVID19. The statistical analysis is good. The conclusion is too brief; it is just a simple repetition of the introduction. Therefore, the conclusion should be rewritten.
Additional comments: This paper provided statistical analysis and established predictors for COVID 19, which may provide valuable tools for the identification of vital status at the hospital discharge. However, this paper has not provided sufficient details of the major outcomes. For example, there is no description of NNet1 and NNet2. If they are general neural network classifiers constructed by the authors, the author should specify the type of them (e.g. RNN or CNN), and provide the details of its hyperparameters, e.g., number of layers. If the authors adopted the NNet from somewhere, the authors should provide where it comes from. Also, as the dataset is not big, the authors should justify the reason to use a neural network as the predictor. Instead of comparing them with a linear classifier, the author should compare the performance of the neural network classifiers with the popular nonlinear classifiers, e.g., SVM. The conclusion is too brief; it is just a simple repetition of the introduction. Therefore, the conclusion should be rewritten.


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 RISK FACTORS FOR MORTALITY ASSOCIATED WITH COVID-19
Review round: 1
Reviewer: 2

Output:
Basic reporting: The biggest issue is the use of a relatively small patient set (N=246) from a cohort with unusually high mortality rate (>17%) and the lack of an independent patient set for validation.

A strength of the study is that it uses a large number of variables (~100) to assess mortality using a machine learning approach. However, there is no clear conclusion whether or not new variables associated with mortality have been identified.
Experimental design: The biggest issue is the use of a relatively small patient set (N=246) from a cohort with unusually high mortality rate (>17%) and the lack of an independent patient set for validation.

Machine learning models were then trained on what I assume is data from 20% of the patients  (i.e. ~50) while the prediction accuracy was evaluated using data from the remaining 80% (ie. ~197). I wonder if this represents a balanced analysis given that only 17% of all patients (i.e. ~8 in the training and ~33 in the testing set)  did succumb to Covid-19 ?
Validity of the findings: The authors show that their neural nets algorithms performed better compared to their linear models when predicting mortality to Covid-19. Interestingly, their NNet1 and NNet2 algorithms partly assessed unique variables e.g. ‘α.hydroxybutyrate.dehydrogenase’ was the second most informative feature in NNet2 (total of 32 variables) while it was not used at all in NNet1 (total of 9 variables).  It is thus unclear to me what this means for the utility of  ‘α.hydroxybutyrate.dehydrogenas’  in predicting risk ? On the contrary, are variables the feature in both models (i.e. lactate.dehydrogenase)  considered to be most predictive for mortality to Covid-19 ?

I would thus encourage to authors to extend their relatively short section which aimed to interpret the results from the NNet1 and NNet2 algorithms.

Most critically, it remains unclear how this model performs on other independent datasets and especially those with lower mortality rates ?
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: IDENTIFICATION OF RISK FACTORS FOR MORTALITY ASSOCIATED WITH COVID-19
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although there are still some typographical errors, the revised document and the response letter seem better. The literature review was good, and the original data was shared this time. A comparative study was carried out using other nonlinear classifiers. My concern is that the NNet1 and NNet2 proposed are not deep neural networks, but their performance is better than most other nonlinear classifiers. The author must provide a convincing explanation in the next round of review. Actually, if the parameters of other classifiers are not adjusted properly, the comparison results may be biased.
Experimental design: The revised version for experimental design is acceptable with methods described in sufficient detail. The revised title more properly reflects the targets of the paper.
Validity of the findings: The revised version addressed most of my concerns. The only issue is the novelty of the paper. Although the data is precious, in terms of classification methodology (normal neural network classifier with existing parameter tuning methods), no significant contribution can be detected. I am not sure whether this is acceptable in PeerJ.
Additional comments: The revised document and its response letter resolved most of my concerns. A comparative study was conducted and the results of other non-linear classifiers were provided. My concern is that the Nnet1 and NNet2 proposals are not deep neural networks, and their performance is better than most other nonlinear classifiers. The author must provide a convincing explanation in the next round of review. In addition, if the parameters of other classifiers are not adjusted properly, the comparison results may be biased.


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: GAMETOPHYTIC SELF-INCOMPATIBILITY IN ANDEAN CAPULI (PRUNUS SEROTINA SUBSP. CAPULI): ALLELIC DIVERSITY AT THE S-RNASE LOCUS INFLUENCES NORMAL POLLEN-TUBE FORMATION DURING FERTILIZATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting paper that addresses gametophytic self-incompatibility in tetraploid Prunus serotina. The subject is relevant since no previous molecular studies have been performed in this subject in this species. The article is easy to read and straightforward.

However, there are some issues that should be addressed to merit publication:
- Literature references. Even if self-incompatibility has not been studied at the molecular level in this crop, some key references are missing in the manuscript. One is a PhD. thesis [Self-and cross-incompatibility in black cherry (Prunus serotina)] from 1969 and freely available at https://ufdc.ufl.edu/UF00097757/00001. Some other references related to the species could be added. For example: Pairon et al., J. AMER. SOC. HORT. SCI. 133(3):390–395. 2008 and others. In addition, work performed in tetraploid sour cherry should also be cited (example Tobutt, K.R., Bošković, R., Cerović, R. et al. Identification of incompatibility alleles in the tetraploid species sour cherry. Theor Appl Genet 108, 775–785 (2004)) since this is relevant to the results presented here.

- Introduction.
•	Arboreal. I would recommend replacing this word in the document by “woody perennial” or similar.
•	Replace “berries” by either “fruits” or “drupes”, which is the correct botanical term for the fruits of Prunus.
•	The ploidy of Prunus serotina should be described with a citation in the introduction section. In addition, information describing the situation of Prunus serotina in the genus Prunus should also be added. (see for example Pairon et al., J. AMER. SOC. HORT. SCI. 133(3):390–395. 2008.).

- Materials and methods
•	Line 86. It is not clear why the authors for the pollination experiments use unknown trees from a private orchard instead of using the same plant material used for the molecular analyses. This should be explained
•	Line 155; change “fertilized pistils” by “pollinated pistils”
•	Line 158. This seems inaccurate since the BBCH scale uses numbers not letters. I assume this refers to the balloon stage which could be either stage 59 or 60.

- Results
•	Figure 5 is of low quality. I recommend improving the quality of the figure so the pollen tubes can be properly seen.
•	Line 267. It is not possible to appreciate swelling of the tip of the pollen tubes in Figure 5a.
•	Raw data of pollen tubes. Looking at the excel file with the number of pollen tubes at different levels of the style, pollen tubes in significant numbers are found at the third level of the style in many incompatible crosses. This should be explained with detail since it is not clear from these data that the crosses are indeed incompatible. Crosses in the field of these combinations should be made to confirm this point.

- Discussion
•	Why only two alleles per genotypes are obtained if the species is tetraploid? Should not we expect some cases with more than two alleles as observed in tetraploid sour cherry?
Experimental design: The paper describes original primary research that falls within the aims and scope of PeerJ.
The experimental design is appropriate to address the main research question and the methods are described with sufficient detail. However, there is a main problem with the results presented since no crosses in the field have been performed and, consequently, we cannot rule out that self-incompatibility is not complete; in fact, in the raw data we can see in several self-incompatible crosses, pollen tubes reaching the base of the style. I recommend performing those crosses in the field.
Validity of the findings: The paper is of value but, in my opinion, it would be necessary to validate the results obtained with crosses performed in the field.
Additional comments: The paper is of interest but it needs to add additional references and properly address the finding of pollen tubes at the base of the style in putatively incompatible crosses; those should be validated by pollinations made in the field of those same pollinations made in the laboratory.


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: GAMETOPHYTIC SELF-INCOMPATIBILITY IN ANDEAN CAPULI (PRUNUS SEROTINA SUBSP. CAPULI): ALLELIC DIVERSITY AT THE S-RNASE LOCUS INFLUENCES NORMAL POLLEN-TUBE FORMATION DURING FERTILIZATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study was aimed at identifying S-Locus encoded S-RNase alleles of P. serotina
and to use this data for identifying compatible accession to overcome self-incompatibility barrier in this species. The authors successfully used S-RNase allele sequences for the identification of S-haplotypes in P. serotine. The paper is well written and experiments are well designed and analyzed. It is interesting finding that tetraploid P. serotina shows cross-compatibility patterns and GSI did not breakdown as a result of hetero-allelic pollens.

I recommend the revision of this manuscript. Here are my specific suggestions and comments for improvement of this manuscript:

1.	Provide the sequence of the primers used for PCR amplification in the Methods section. Currently, there are two back-references used [PaConsI-F (Sonneveld et al. 2003) and EM-PC5consRD (Sutherland et al. 2004) primers]. The primers should also be mentioned in the legend of the figures/supplementary figure (gels), so that it becomes an independent and easily accessible entity.

2.	Are these 15 P. serotina accessions used in this study available in any germplasm bank for other researchers? please give details of their availability and passport data. This information should also be provided /updated with the sequence accession numbers in the NCBI.

3.	Some repetition in results and discussion sections can be avoided (for example line 274-285 as previously described in results).

4.	Table 4:  contains proposed crosses according to the S-allelic composition of the 7 P. serotina trees genotyped with an expected outcome. The authors can add one more column of the results from crossing. It makes sense to compare results with their hypothesis.

5.	Figure 4: Gel images need better annotations. The gel lanes should have marked for the restriction enzyme used corresponding to each lane. It is very difficult to go back and forth from Table 1 to figure out what is actually going on in the figures. The S alleles numbers are not organized and are haphazard that adds an extra complication to the figures.

6.	Figure 6: the text of sequence alignment should be larger and legible.

7.	Supplementary_File_Raw_Data_1: Column labels should be descriptive: what do you mean by First Third/ second Third/ Third Third: is this the # of the cross showing pollen tube growth along the style length. A legend on the Top of the Supplementary Table will be useful.

Are these replicates? are these parallel experiments. What the numerical count means (seeds or pollen tubes?).

8.	Supplementary_Uncropped_gels: each of the gel’s pictures needs an independent label and legend and they should be labeled properly.

9.	Table S1: DNA sequences for all S alleles are in the NCBI GenBank database (accession numbers: MN098833-MN098846): Checked
Experimental design: -The experiments are well designed and analyzed.

-This manuscript extends the S-haplotype mapping to additional accessions. The concepts and findings are not novel.

-Methods are described in sufficient detail.

-Additional information on the primers and information about the availability of the germplasm from 15 accessions of P. serotina will benefit the research community. Such information and relevant passport data should be updated to sequence submitted to NCBI.
Validity of the findings: -All relevant data is provided and conclusions are well-drawn.

- The figures and supplementary figs need improved labeling and legends for legibility.
Additional comments: The authors successfully used S-RNase allele sequences for the identification of S-haplotypes in P. serotine. The paper is well written and experiments are well designed and analyzed. It is interesting finding that tetraploid P. serotina shows cross-compatibility patterns and GSI did not breakdown as a result of hetero-allelic pollens.


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: GAMETOPHYTIC SELF-INCOMPATIBILITY IN ANDEAN CAPULI (PRUNUS SEROTINA SUBSP. CAPULI): ALLELIC DIVERSITY AT THE S-RNASE LOCUS INFLUENCES NORMAL POLLEN-TUBE FORMATION DURING FERTILIZATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have successfully addressed my previous comments on the manuscript.
Experimental design: The authors have successfully addressed my previous comments on the manuscript.
Validity of the findings: The authors have successfully addressed my previous comments on the manuscript.
Additional comments: The authors have successfully addressed my previous comments on the manuscript.


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: GAMETOPHYTIC SELF-INCOMPATIBILITY IN ANDEAN CAPULI (PRUNUS SEROTINA SUBSP. CAPULI): ALLELIC DIVERSITY AT THE S-RNASE LOCUS INFLUENCES NORMAL POLLEN-TUBE FORMATION DURING FERTILIZATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clear and concise.
Experimental design: Methods have been described sufficiently
Validity of the findings: Supported by data and well-articulated.
Additional comments: All the previous suggestions have been addressed.


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: MIMICKING PROPHAGE INDUCTION IN THE BODY: INDUCTION IN THE LAB WITH PH GRADIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Mimicking prophage induction in the body: Protocol for induction in the lab with pH gradients by Miller-Ensminger et al is a streamlined proof-of-concept methods description of inducing prophages from lysogens using pH. While the lysogens were isolated from human bladder, it is likely the methods are widely applicable. The method is timely, in that the need to study the influence of prophages (and their lysogens) within microbiomes is rapidly being recognized.

Overall, the writing style is clear and concise. In some areas, however, a few grammatical errors creep in that need to be addressed with a careful read through.
Additional minor improvements are suggested below.

One concept may need clarification: I appreciate the idea that distinct niches provide unique growing environments, including pH, for the microbes that inhabit them. However, in most cases the microbes are adapted to those conditions (e.g., pH) and thus it is likely that deviating from that pH, for example, is stress that mediates the induction. If so, maybe make that more clear to the reader?
Experimental design: Concise. Some clarity needed. For example, In Step 2 (i), please define shaking (what speed?). Orbital shaking speed is often important.

Please also define what 'overnight' means. Does it matter if the bacteria grow for exactly 18hrs? Is the intention to subculture the bacteria while still in log phase or in stationary phase? This may influence induction.

Step 3 (iii), is the LBSA a low melt variety? If so, which one? How low did you bring the temperature down from 65C before mixing and overlaying the soft agar?
Validity of the findings: The findings are clearly reported. The rationale for the study is clear; all data have been provided.
Additional comments: Some additional comments:

Cat is defined in Table 3, but appears first in Table 1.
Table 1 needs a better description. Define "cat" but also make it clear that the number represents the number of predicted prophages.

Table 2 legend: change "platting" to plating.

Figure SF1: needs a legend --when was the OD taken? The legend should emphasize reduced growth/viability of the E coli since it does not do well at the pH extremes.

Table 2:  spot assays were repeated 3 times? If so, this notation (+/-/+) means the second experiment failed to produce a clearing?
Spot assays are notoriously problematic, so the reader should be warned. Especially in a situation like this ( -/-/+)-- why did it fail to produce a clearing the first two times?

The differential induction noted in lines 279-281 is an important observation; maybe suggest to the reader followup strategies to quantify this observation?

In line 233, for TEM, was the supernatant concentrated in some way? It would seem the prophage particles would otherwise be too dilute to visualize on the grids.


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: MIMICKING PROPHAGE INDUCTION IN THE BODY: INDUCTION IN THE LAB WITH PH GRADIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, this is a well-written paper.  It has a very good introduction which is thoroughly referenced.  The induction method is clearly described overall and may be very helpful for researchers who wish to avoid mitomycin C either due to its cost or safety issues.

The results and discussion are not as extensive but are acceptable for a methods paper.  Key points of the results are discussed.  This method is not completely novel, as the authors clearly acknowledge, but a good methods summary is still a useful publication.

There are two minor typos that should be corrected.  In line 159, the second use of LBSA is misspelled as “LSBA”.  In the legend for Table 2, it should be “plating” not “platting”.  Or “spot testing” which is a common way of naming this procedure.
Experimental design: This is not an entirely novel method as the authors state, so it isn’t filling a knowledge gap.  But it is filling a procedural gap.  Due to the growing popularity of phage therapy, more researchers are beginning to work with phages.  Practical methods papers such as this one are worth publishing to help new workers in the field.  As well, as the authors note, this method might be effective with other types of bacteria in other environments so this article has the potential to be more broadly applicable.  This would have to be tested experimentally of course.

Overall, the methods are very detailed and clear.  They should be accessible to experienced and novice phage biologists.  There are a few minor revisions needed.

Revision 1.  One procedure requires some clarification.  In Step 4. ii. (line 178) and Step 4. xi. (line 192), the protocol states that the recovered top agar containing phage is vortexed for 10 minutes.  Given that most vortexers are capable of mixing at 10’s of rpms to DNA shearing speeds of 1000’s of rpms, some indication of the shaking speed should be indicated.  I presume it is in the 100’s of rpms but this should be stated.

It isn’t clear to me why this step is being performed except perhaps to speed the process of phage release from the agar.  In my lab, we typically just leave cored plaques sitting in buffer for 30 minutes to 2 hours with no shaking and get good phage recovery.  No change in the paper is needed around this point except for the added detail of rotation rate.

Revision 2. A second detail that should be added is in the optional task in lines 197-198.  When trying to obtain a pure strain of bacteriophage from a potential mix, more than one round of passaging is recommended.  Adams (Bacteriophages; InterScience: New York, NY, USA, 1959) recommends 3 rounds of passaging while Lobocka and colleagues (The First Step to Bacteriophage Therapy: How to Choose the Correct Phage. In Phage Therapy: Current Research and Applications; Borysowski, J., Miedzybrodzki, R., Gorski, A., Eds.; Caister Academic Press: Norfolk, UK, 2018; pp. 23–67) recommend 5 rounds.  In either case, one round is not sufficient especially if the plaque density is high as shown in Figure 2B. This should be noted in the text.

Revision 3.  Regarding Figure 2B, if it is possible to replace it with a photograph of a plate with a more dilute sample to give a lower plaque density, this should be done.  It would be better if the plaques are distinct and rarely overlapping so that the plaque morphology is clearer.  The current picture appears to have multiple plaque types although Table 2 only lists a single phage from the indicated E. coli strain.
Validity of the findings: No additional comments for this area.
Additional comments: This is a nice method.  I have students trying to isolate phages right now and mitomycin C was our backup plan if we needed to induce prophages.  We may try your method as well.

Fun fact only distantly related to this paper, the FDA recently approved a mitomycin gel for treating urothelial cancer (https://www.fda.gov/news-events/press-announcements/fda-approves-first-therapy-treatment-low-grade-upper-tract-urothelial-cancer) so the types of E. coli used here may be exposed to mitomycin “in the wild” and presumably have phage induction occur.  Perhaps urine from patients undergoing this chemotherapy could be a new source of phages.


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: DESCRIPTION OF A NEW SPECIES OF CRYPTIC SNUBNOSE DARTER (PERCIDAE: ETHEOSTOMATINAE) ENDEMIC TO NORTH-CENTRAL MISSISSIPPI
Review round: 1
Reviewer: 1

Output:
Basic reporting: Animal usage and permitting descriptions are presented and seem appropriate. Well written and depth of literature looks good. Figures seem fine.

New species:
New species name is not in title, but it is in the abstract.
New species has been entered into ZooBank according to methods. However I was unable to locate it with the link provided. Presumably because this paper is not accepted yet.
I honestly can judge whether it meats ICZN standards. However they do provide a generally recognized (modern) species definition that they are applying.
Experimental design: This paper is essentially a follow up to a just published genetics paper (DOI 10.7717/peerj.9014) where they suggest that there is a cryptic species present. Here, the authors present a detail phenotypic analysis to quantify and determine support for the species diagnosis and provide a taxonomic description. There was no detected flaws or concerns with the methodology or design of the study.
Validity of the findings: I think the findings are valid, however there is always the nagging feeling that it is too easy to pick a species definition that fits the data.
 One thing that I struggled with was 1) the lack of (even a brief) description of what the unified species definition is (criteria), and in the discussion you don't clearly link your findings to said criteria. This would be valuable for some readers.
Additional comments: Line 453-458 you write "..quantitative differences in lateral line scale..color... length...and morphology...support the recognition of ... valid species"
Line 470 quantitative differences we detected are similar to those found for other species of snubnose darters"
If the timing of divergence is recent relative to other snubnose darters sibling or sister taxa, are you saying that faulkneri and raneyi display phenotypic divergence comparable to other examples of more deeply diverged taxa? If so, perhaps a more specific reference to examples would be warranted in the discussion, as this would help to clarify/strengthen your argument for species recognition.

Line 98- closed parenthesis is italicized at end of sentence.

Line 455 remove space after "Figure 6"

RE: Table S1. "Estimated stream gradients and watershed area for Yazoo Darters in the Yocona (Y.R.) and Little Tallahatchie (L.T.R.) River drainages."
Should be 'Yocona River and Little Tall.. River drainages' - or - 'Yocona and Little Tall.. river drainages' (where river is lower case in reference to both names)


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: DESCRIPTION OF A NEW SPECIES OF CRYPTIC SNUBNOSE DARTER (PERCIDAE: ETHEOSTOMATINAE) ENDEMIC TO NORTH-CENTRAL MISSISSIPPI
Review round: 1
Reviewer: 2

Output:
Basic reporting: Custom checks:
Ethical treatment of organisms covered under University of Mississippi IACUC (protocol 09-027).
The experiments (capture and photographing of fishes) were necessary to the study, however, the treatment of the photographed fishes is not stated (See ED below).
Appears to be a discrepancy in field collection permits, and this is probably due to omission of information in the text. In lines 54-56 it states that field collections were made using permits for the years 2009-2014, however, line 65 states that collections for photographs were made in 2017-2018.  (See comments by line below).

Basic Reporting:
In general, clear, concise and well composed, however, there are some areas of ambiguity due to omission of information, awkward sentence structure or information not being organized in standard scientific format. The paper has an excellent foundation based on pertinent citations.  One area that poses the greatest difficulty is the figures and tables.  They are a bit of a mess when it comes to captions, legends and even omissions or correct information (e.g. Figure 1).  I will list the figures and table problems in a subsequent list.  Unfortunately, my computer would not open the raw data file(s).
Experimental design: Experimental Design:
This appears to be an original work based on a foundation of earlier endeavors.  The subject is one that is well founded and in dire need of discussion.  It is a very important addition to our understanding of diversity of freshwater fishes.  The overall design is sound, however, there could (should) be additional statistical analyses performed.  There is some confusion regarding methods. Once again, generally good, but some important details are lacking (e.g. Where the fishes that were photographed for nuptial coloration evaluation, anesthetized and released, or were they euthanized and preserved?).  More specifics and their
Validity of the findings: Validity of Findings:
I was unable to assess the raw data.  But there are minor inconsistencies in data description. Some of which may stem from inadequate captioning on figures and tables.  This is a problem that was consistent for all tables and figures.  Most importantly, their conclusion that Etheostoma faulkneri is an undescribed species confused with E. raneyi is well supported by their results.

It is a very important paper increasing our understanding and accounting of biodiversity in the southeastern U.S. and worldwide.  Also, it is imperative for the conservation of this species.
Additional comments: General Comments:
A sound piece of research presented in this manuscript is deserving of Acceptance for publication with moderate revision which includes minor composition issues, organization and a need for further statistical testing (Calculation of 95% Cis are not sufficient to determine significant difference.  Statistical analysis resulting in p-values is in dire need).
Below I list potential edits or issues line by line and for all figures and tables.

Lines:
27: Follow Upper Gulf Coastal Plain with abbreviation (UGCP).

34: Same as line 27 follow with acronyms or abbreviations i.e. (LGCP) and (MAP)

37-41: What is the genetic distance between lineages that has be found and what model was used.  May want to not include this here but rather in lines 321-322.

55-56: The collecting permit discrepancy noted above.

58-68: Male nuptial color photos of live fishes. Were the fishes preserved or were they released. Was MS222 or the like used. I found the answer in the Supplement, but it needs to also be stated in the manuscript text.

69-82: Experimental design fine except perhaps the limited number of participants “colleagues” (only 3)

70-71: what was the sample size of darters photographed.

89-93: Differences in modal counts from literature “adjusted”. How? Please explain how adjustments were determined. Were the same fishes (museum specimens) observed by different authors?

96: “28 pairs of points” – very ambiguous as to what represents a pair of points that was measured. See Table 10 referred to in Figure 2 (not anywhere in the text at this point).. This is like a treasure hunt trying to find pertinent information in ms. This information should not be buried in a figure caption. Table 10 should be Table 2, chronologically if mentioned in text instead of referenced in figure 2.

98: “checked “ replace with assessed

99: “showed” replace with had

99-101: Why was the data not fully treated statistically using something like ANCOVA, also PCA or its equivalent.

106: “so” change to thus

109: citations for traditional multivariate needed to justify use of “morphometric”

107-113: Justification to use “morphometric approach” deemed appropriate, however, the phrase “morphometric” is ambiguous because there are many morphometric approaches used by systematists. Possible edit “ a morphometric approach as first described by Bookstein (1991) and subsequently modified (Parsons et al., 2003…
107: Possibly abbreviate geometric morphometric analysis as GMA.

119: On figure 3 I can only find 18 landmarks.

137-142: no statistical testing of means, p-values.

150-151: In Supplement it states fishes were released, or were they part of your collections (line 148)?

144: Now using phase “morphological analysis”. What does this include Truss, GMA, etc…?

148-149: Brings up question once again of how your specimens were handled, killed/euthanized, preservation techniques…

172: See comments on figure (#4).

174: No p-values to determined for testing significant differences, no stats other than 95%CI; See comments on caption and figure (#5)

177: 17.7% of what, no sample size reported.

182: See comments on table 3

193: GMA previously called morphological analyses on line 144?

201-210: A point alone cannot be longer or shorter, needs reference to some other point; reword

205-217: Since a large percentage of individuals are mis-identified from wrong drainage or wrong sex a multivariate plot (e.g. PCA) would be a helpful figure to include

227 replace > with greater than

226: Cannot make this conclusion from the data presented. Need actual hydrologic data (i.e. discharge)

230: add Synonomy

275: insert mm after 41.2

250-268: Don’t think the parenthetical information is needed in a synonomy.

296, 299: Un-named, lower case, not a proper noun

308: (Table S2), S is not defined.

311: Lat line scale counts differ, are they significantly different?

320: remove “overall” at end of sentence

321-322: What is the genetic distance and model used.

323-326: New paragraph

328-329: Why is no “mode” listed for transverse scales and scales around caudal peduncle?

341-342: insert “margin” after dorsal fin and delete “on the fin margin”

343: replace “there is no” with “we did not observe a”

352: Not clear what you are talking about, I do not see it  (fig 4)

371-372: On Fig 4 I do not see a dark or dusky suborbital bar.

386: is somewhat redundant with line 380

425: Did not read anything about genetic dversity

427-429: Awkward sentence

436-437: Spell out all first use of acronyms; we are not all Feds.

444-: Etymology Very nice!

509: ?

514: remove “the” before lab

Figures:

1. Colored lines are not consistent  from legend to map

2. insert (1-27) after landmarks and remove “is shown”.

3. replace “shown” with “indicated by numbers 1-18”. And if someone sees this figure in greyscale they will not be able to find #16

4. Rearrange completely. Label male holotype as “a” and move photo to top position; female allotype as “c and move appropriately.  Change “d” to “b” and “b” to “d” . Also, put 1cm on black bars. They look like something has been marked out.

5. sample sizes should be reported in main text. The colors of the bars should be more distinctive so that one viewing in grayscale can see the difference.

6 and 7. Move legend for rivers into text of caption. Replace “Output from” to “Results of”.

8. Put a before b in caption!

For figures and tables the captions should contain all information needed to understand the figure or table without having to refer to the text of the paper. Yours tend to be lacking in pertinent information and do not use “shows” or “shown”.


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: EFFECTS OF COWPEA MILD MOTTLE VIRUS ON SOYBEAN CULTIVARS IN BRAZIL
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors addressed the effect of CPMMV isolate from Brazil on few soybean cultivars in different geographical locations. The result showed that CPMMV infection reduced crop yield and affected other agronomical traits, especially when a cultivar doesn’t show clear symptoms of infection.

The introduction need more details in terms of the following:
1)	I suggest authors to add more description about the Cowpea mild mottle virus: ssRNA(+), genome length, virion types, ORFs encoded.. etc.
2)	Also, adding literature about soybean cultivars that have been reported to resist CPMMV would enrich the introduction. Some of the examples I found are listed below, and pretty sure authors can enrich the introduction with more information.
•	https://doi.org/10.1111/pbr.12455
•	https://doi.org/10.2135/cropsci2012.01.0042
Also adding some discription (in terms of virus resistance) of the tested cultivars would be of good addition.
Experimental design: On the experimental level, the manuscript can be significantly improved with a few extra works to carry out:

1)	Partial sequence may not give a sufficient idea about the distance to other isolates. I encourage authors to fully sequence the CPMMV isolate and generate a phylogenetic tree with other known isolates of CPMMV strains. For example, some ORFs of few soybean mosaic virus strains share 100% identity, such as those in G5H and G7H strain, but their strains’ pathogenicity is different in few cultivars. I encourage authors to fully sequence the isolate they have.

2)	Test the susceptibility of those cultivars in lab conditions where temperature, light, humidity and other factors are fixed.
Validity of the findings: 1)	It will be of valuable addition if authors provide information about the climatic and geographical differences among the regions used in this study.

2)	Compare the susceptibility of those cultivars depending on the region.

3)	Please clarify the difference between symptomatic vs asymptomatic infection in terms of agronomic traits including crop yield.
Additional comments: I hope that authors address the experimental points in the revision so the manuscript can have better structure and results that are interesting for wider number of audience.


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: EFFECTS OF COWPEA MILD MOTTLE VIRUS ON SOYBEAN CULTIVARS IN BRAZIL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The english language is clear and unambiguous. The manuscript structure is conform to Peer J. The summary is clear in succint. The number of tables and figures is appropriate and their quality adequate. The caption/legends contain sufficient information. The references are appropriate.
Experimental design: The introduction state the scientific problem clearly. The materials and methods used are adequate for the problem under investigation and sufficiently well documented. The statistical treatment is adequate.
Validity of the findings: The manuscript provide important new information on the effects of CPMMV to Brazilian soybean production and the abilty the Brazilian CPMMV to be transmitted by seed. The experimental procedures are competently conducted even if field trials were not repeated. Conclusions are well stated.
Additional comments: I consider the manuscript worthy for publication subject to the minor corrections and suggestions provided below. The title sound like a review and need to be improved.
Suggestions
Title : Effects of Cowpea mild mottle virus on soybean cultivars in Brazil
Lamas et al (Plant disease 101, 2017, Vol 10) shown that CPMMV was also detected in Sida sp (Malvaceae) and for the first time CPMMV was found in uncultivated plants belonging to several botanical families. Please include it in Lines 68-69 and complete your references.
Add one column to the table for the yield loss


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: DOUBLE LIVES: TRANSFER OF FUNGAL ENDOPHYTES FROM LEAVES TO WOODY SUBSTRATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the material is well-written, and the experiment represents a novel contribution.
Experimental design: I have a few more substantial comments about the rationale for analysis and presentation of methods (see below in comments to author)
Validity of the findings: All of the data has been provided, meaningful replication was used, and the conclusions drawn from the paper are clearly linked to the Foragin Ascomycete/viaphyte hypothesis that the authors laid out in the beginning of the paper.
Additional comments: In this paper, the authors present evidence that some fungi may have a functional strategy wherein they exist inside plant leaves as endophytes in order to colonize dead wood or leaf material upon leaf senescence. The authors refer to this idea as the Foraging Ascomycete Hypothesis, or the “Viaphyte” hypothesis. Interestingly, the authors primarily focus on the possible benefits of a life history strategy for the fungal symbionts, rather than focusing on plant life history strategies or why plants may have evolved to host microbes. Overall, the material is well-written, and the experiment represents a novel contribution. I do have a few more substantial comments about the rationale for analysis and presentation of methods, in addition to some minor line comments below.

Major Comments

1)	Important methodological details for molecular work and statistical analyses are not presented in several cases, as follows. L136-141 – Please provide all conditions for PCR and PCR clean-up if it was performed. L142-144 – What were the parameters or criteria you used for sequence trimming and OTU/Taxonomic grouping? L150-156 – Please describe statistical analysis methods in more details, as written no mention of linear models, random effects, or post-hoc tests used are given.
2)	L147-148 – Why did you curate the UNITE database to only the genus level??? I understand that you wanted to use the FunGuild database (which requires genus to give an assignment). However, microbial taxonomic classification methods are not perfect, when you so substantially alter the database you are using as a reference for name assignment you are bound to overclassify microbial taxa when the true expected taxa are missing from the reference database. I do not believe that the desire to use FunGuild in this case warrants such a severe restriction of the reference database. FunGuild functional assignments should always be considered only as potential evidence of function. There is clear evidence in the literature of single fungal genera encompassing multiple life history strategies at the species level. (also Lines 167-8, 204-5).
3)	L231-238 – This paragraph seems an important place to mention that future experiments should empirically test the ability of “viaphytic endophytes” to invade woody substrates when there are other colonizers already present. Your current experiment is fairly far removed from real conditions (sterile tongue depressors), and thus more realistic experiments are worth mentioning.

Minor Line Comments
L123 – Don’t say Roy Lab, just say were brought back to our lab at U of O for processing.
L134 – why was only a single morphotype sequenced? Can you be sure of your accuracy in morphotyping, or how frequently did you use microscopic features to assist your identification?
L170 – As written, this sentence is confusing. The fungi were isolated from wood not leaves yes? You can’t really comment on the number of taxa isolated from leaves, it is really the number of taxa found on wood that presumptively came from the same leaf group.
L185-188 – Please make it clearer what the N= stands for, is this the total number of all isolates from a box and then we take the percentage to get the final number per species, or is the N= the number for species?
Figure 1 – There are 5 isolates on the right-hand side of the figure that are noted as being cultured from 1 leaf, yet there are no isolations of these taxa? These do not appear to be the same 5 taxa mentioned in the figure legend as being unidentified, or this is confusing if they are. Please clarify on both counts to make this figure interpretable.