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: DIFFERENTIATION PATTERNS OF EMPEROR MOTHS (LEPIDOPTERA: SATURNIIDAE: SATURNIINAE) OF A CONTINENTAL ISLAND: DIVERGENT EVOLUTIONARY HISTORY DRIVEN BY PLEISTOCENE GLACIATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is in general clearly written, although there are some grammatical mistakes that could be cleaned up. I did not keep track of them.
Experimental design: This is a very interesting topic, and certainly worthy of investigation. The authors have looked at the divergences of species of Saturniidae moths in Taiwan compared to conspecifics or congeners on the mainland. They base their findings on three loci (2 mitochondrial and one nuclear). I have to say I was a bit surprised by their choice of markers, COI is obvious, but why 16S and 28S? If one looks at the Lepidoptera literature, there are a number of other widely used markers (EF1a, wingless, GAPDH, RpS5, etc) that would have made more sense to sequence in a PCR based study. What's done is done however.

Another surprise was that the authors chose to do a NJ analysis for the combined dataset, as well as a Bayesian analysis. If I understood correctly, the tree shown in Fig 2 is the NJ tree, why is that? It has been shown time and again that NJ is not a particularly good method for estimating phylogenetic relationships, and it would be preferable to report the results of a maximum likelihood and/or Bayesian analysis. The deeper nodes seem to have no support from the Bayesian analysis, is that because the topology was different? Outgroups are reported to be saturniids in related subfamilies, however the tree in Fig 2 has Bombyx mori and the sphingid Theretra, distant relatives to Saturniidae (with 3 markers, maybe too distant). I would suggest rerunning the phylogenetic analyses with IQ-Tree and MrBayes with appropriate outgroups.

Finally, the use of a molecular clock rate for the timing of divergence analyses, especially a rate that was estimated 25 years ago based on minimal data, is perhaps not the way to do things in the 2020s. Why have the authors not attempted to estimate times of divergence based on calibrations from published studies? E.g. Kawahara et al (2019, PNAS) include Attacus, Saturnia, Actias, and Hemileucinae representatives. Their estimates for times of divergence of these lineages can be used as secondary calibrations in the authors own dataset to get estimates of COI rates for each genus separately. Very easy to get these values from BEAST. This would not change the qualitative results of the different lineages having different times of divergence, but the quantitative results will likely change (the times of divergence).
Validity of the findings: The main findings, that different lineages have different histories, with some lineages diverging from mainland lineages a long time ago, vs those lineages that are still very close to mainland lineages, will probably remain after re-analysis of the data. This is an interesting result, expected to some degree, but good to show. There are also some surprises with e.g. the Attacus lineages being so divergent form each other.
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: DIFFERENTIATION PATTERNS OF EMPEROR MOTHS (LEPIDOPTERA: SATURNIIDAE: SATURNIINAE) OF A CONTINENTAL ISLAND: DIVERGENT EVOLUTIONARY HISTORY DRIVEN BY PLEISTOCENE GLACIATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is my second review of the manuscript titled "Differentiation patterns of emperor moths (Lepidoptera: Saturniidae) of a continental island: divergent evolutionary history driven by Pleistocene glaciations".

Overall, the authors have accurately addressed the previously raised concerns.

I noticed however that the study is restricted to the subfamily Saturniinae (line 181), but througout the manuscript the authors refer to their study subjects as "saturniids" or "saturniid species", which would refer to the family level. To be more precise, the adjectival form of Saturniinae is saturniines or saturniine species.

line 63: "evolved with a unique differentiation pattern" - can you be more specific? Are we talking about timing, geneflow, geographic connections or more theoretical concepts like allopatry/parapatry etc? And how are they specifically different from those in the Amazonian regions?

The aforementioned suggestions should be easy to incorporate and with those I recommend the manuscript be accepted for publication.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: DIFFERENTIATION PATTERNS OF EMPEROR MOTHS (LEPIDOPTERA: SATURNIIDAE: SATURNIINAE) OF A CONTINENTAL ISLAND: DIVERGENT EVOLUTIONARY HISTORY DRIVEN BY PLEISTOCENE GLACIATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revision is a much improved version of the manuscript. The grammar is now fine. Spelling of scientific names should be double checked, I noted the following misspellings:

Line 250 Antheraea superb --> superba
Lines 323+420 boisdubalii --> boisduvalii (also in Fig 7)
Line 396 aturniid --> saturniid

There may be more.
Experimental design: I accept the authors argumentation that the relaxed molecular clock using secondary calibrations did not work as expected. An interesting observation, but I guess it is known that one cannot use the same clock models for intraspecific vs interspecific analyses in the same dataset. As it is, the strict molecular clock analyses are probably in the right ball park with regard to times of divergence.
Validity of the findings: The findings are interesting and increase our understanding of how fauna develop over evolutionary time. Even if the estimated times of divergence are not exact, they still tell the story of different histories for the different taxon pairs.
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: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The family Saturniidae is importantly economic insects used for silk-producing or edible species. However, information regarding African Saturniidae is very limited. This study provides 12 new complete mitochondrial genomes of African Saturniidae species and offers a well-resovled phylogenetic relationships in the family. The introduction into these species and why they are interesting is done well. The papers is well written the data seems to support the conclusions. Before acceptance for publication, some points should be addressed.
1. I suggest that the authors can provide the accession nos. (in GenBank) of 12 new mitochondrial genomes in Table 1.
2. I commend the authors to perform a DNA barcode analysis for 12 Saturniidae species with the known vouchers in BOLD system (www.BOLDsystem.org) and GenBank to ensure that the samplings are right. By searching against BOLDsystem and GenBank, only two species, Nudaurelia wahlbergii and Vegetia grimmia, have not available DNA barcode sequences.  Thus, I ask authors to please submit the DNA barcode of the voucher used for the mitogenome to BOLD, along with its metadata (collecting data, photo,….).
3. If possible, please perform a search for tandem repeat element in the A + T-rich region, as found Antheraea pernyi and Antheraea roylei.
4. Line  28: Bayesian = Bayesian inference.
5. Line 66. mitochondrial genome = mitochondrial genome (mitogenome).  Please check throughout the text.
6. Line 82. Please provide a reference for the number of 24%.
7. Line 108. What is the size of the NGS reads?
8. Line 181. The ancestor type for non-Ditrysian lineage Hepialoide of Lepidoptera has been reprted by Cao et al. (2012) [BMC Genomics 13, 276].
9. Line 219. maximum likeihood = ML.
10, Some references are repeated.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The model name GTR+G+I is generally not preferred, please change it to GTR+I+G.
Please mention the accession number PRJNA796275 in the main manuscript.
Experimental design: The authors find largely consistent phylogenetic relationships among BI and ML analyses. The problems happened in Saturniini especially for the positions of Cricula trifenestrata and Neoris haraldi. They attribute the inconsistency to low quality of the mitogenomes of the two species. It should be noted that the low quality of sequences not only influence the related species themselves but also disturb the whole phylogeny, since the total validate sites will be reduced with erroneous alignments. If it is the case as the authors mentioned, it is worthy to try to rebuild trees without the two species.
Line 105. Do you filter the low quality reads?
Line 162. Please mention how you check and guarantee the completeness of the mitogenomes.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: First of all, I think Authors rational to perform this study, experimental design and its execution are decently reflected in the manuscript. Nethavhani and colleagues sequenced the complete mitochondrial genomes of 12 species found in Southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family. These results support the monophyly of the tribes Attacini, Bunaeini and Micragonini and the placement of E. trimenii and R. fugax in the tribes Eochroini and Attacini, respectively.
This will help to significantly expand the genetic data of Africa Saturniidae and thus provide a more comprehensive understanding of the diversity and relationships among African Saturniidae. Hence, it certainly deserves publication with some moderate changes as below:

1. The mitochondrial genome of Heniocha apolloniais has been determined, but why not put its picture in Figure 1?

2. Some of the statements in Table 1 and Figure 1 seem to be inconsistent.
In Table 1: Vegetia grimmia (Geyer, 1832)；Nudaurelia wahlbergii (Boisduval, 1847)；Heniocha dyops (Maassen, 1872) and Gonimbrasia tyrrhea (Cramer, 1775), but in Figure1: Vegetia grimmia (Geyer, 1831)；Nudaurelia wahlbergii (Nudaurelia, 1972)；Heniocha dyops (Maassen, 1886) and Gonimbrasia tyrrhea (Cramer, 1776).

3. Line 212-214，“Relative synonymous codon usage (RSCU) was higher than 1.0 for all codons and highest for Leu1 (Fig. 7). Average Ka/Ks was less than 1.0 in all PCGs across all species indicating purifying or stabilizing selection and was highest for ATP8 (Ka/Ks = 0.31) (Fig. 8). ” Does the position of Figure 7 and Figure 8 seem to be reversed? What do the black dots in Figure 8 mean? Consider whether it is necessary to annotate.

4. There are still some minor problems in the format of the full text, please check carefully again, for example, there are no blank lines in reference 395-401; Some species names are not italicized, such as Samia cynthia ricini in line 41, etc.


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: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all of the comments.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 2
Reviewer: 2

Output:
Basic reporting: Well written.
Experimental design: Well done.
Validity of the findings: Well done.
Additional comments: I am satisfied by the revision. All potential problems related to my previous comments / suggestions are appropriately resolved. I suggest accepting this paper.


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: MITOGENOMICS AND PHYLOGENETICS OF TWELVE SPECIES OF AFRICAN SATURNIIDAE (LEPIDOPTERA)
Review round: 2
Reviewer: 3

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


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

Input:
Title: HOW MANY SINGLE-COPY ORTHOLOGOUS GENES FROM WHOLE GENOMES REVEAL DEEP GASTROPOD RELATIONSHIPS?
Review round: 1
Reviewer: 1

Output:
Basic reporting: The references are current for the topic, and the figures are clear and of sufficient quality to enhance the article. The results match the hypothesis.
Experimental design: The intent and purpose of the paper is clear. The methods are outlined and replicable. This work is original.

I am not quite sure what the authors mean in the methods when they say “I species missing etc” and in figure 2, this needs to be explained in more detail as to what these species are exactly
Validity of the findings: While this paper presents an alternative hypothesis on the basal arrangements within the clade they are addressing, this fundamentally is a shift in the position of the basal taxa rather than a reorganisation of the branches per se. I have a concern in that the lack of use of similar outgroups may skew the result in the authors’ favour, and that a better method would be to include the same outgroups that the prior study that they seek to overturn had included.

Changing the included outgroups, in case omitting the Scaphopoda and the Cephalopoda (see Cunha and Giribet 2019. DOI 10.1098/rspb.2018.2776), may articfically support the authors hypothesis and indicates a possible selective bias in inclusivity of taxa to gain desires outcomes.
Additional comments: The first paragraph is a but "fluffy" and "waffly", and detracts form the quality of the over all paper.


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: HOW MANY SINGLE-COPY ORTHOLOGOUS GENES FROM WHOLE GENOMES REVEAL DEEP GASTROPOD RELATIONSHIPS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The early-branching events of the gastropods are indeed difficult to resolve, and is a long-standing question whose resolution would help malacologists in many aspects. If this study does not definitely solve the problem, it provides a nice correlation between the size of the dataset used and the topology obtained, and thus provide some guidelines for future studies. I have 2 major comments but, once considered, I think that this manuscript deserves publication in PeerJ:
1. The detection of the SOG is clearly one of the key-point of the methodological approach. Indeed, non-SOG genes would clearly biased the results, as the addition of more and more genes would also mean the additions of more non-SOG genes, and thus a bias in the resulting species trees. However, nothing is said about how the potential multi-copy and/or paralogues were detected. The approach proposed by SonicParanoid should be detailed a minimum. Also, it would have been interesting to check in the single-gene tree any trace of paralogy (i.e. well-established clades – e.g. caenogastropods, heterobranchs,… - that are not recovered monophyletic).
2. The dataset has been designed to match the dataset of Chen et al’s, but I think that updating the dataset with recently published genomes would be actually more interesting, even if it prevents a direct comparison with Chen et al’s tree. Furthermore, the inclusion of C. consors, as noted by the authors, clearly impact the size of the dataset, and I am not convinced that it is useful to maintain it in the study. Or if the goal is to test the impact of low-quality genome(s) on the size of the dataset, this should clearly be stated in the introduction as a goal of the study, and discussed accordingly (including the impact of other “low quality” genomes).
I am providing below a list of other minor points, plus more details on these 2 major comments.
L51: “gastropod types”: types is quite a vague concept… “species”, or “groups”?
L67-68: it is not very clear why the examples provided here are limited to quite narrow subgroups (in comparison with gastropods). Why not simply state that the phylogeny of shallow taxonomic levels has been tackled successfully in many groups, giving a few examples in each subclass?
L74: it seems to me that the close relationships of Neomphalina, Cocculiniformia and Vetigastropoda has been quite clearly demonstrated (eg. Lee et al 2019 - Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny), and it does not seem to be controversy…
L83: see also Smith et al 2011 - Resolving the evolutionary relationships of molluscs with phylogenomic tools.
L115: why was it important to use the same dataset as Chen et al 2020? Why not using more recently published genomes? In particular, the chromosome-level genome of Lautoconus ventricosus instead of the poorly assembled Conus consors genome? The methodological approach could have been the same (except the direct comparison with the tree of Chen et al L178 – see below), but the final dataset could have been much better (in particular more SOG when missing species are allowed). From Fig 1 it is clear that Conus consors is the genome responsible for most of the loss of genes as more missing species are allowed.
L137-138: C. consors is finally removed from the dataset… Why not simply removing it from the manuscript? Or replacing it with Lautoconus ventricosus…
L139: it is not clear if the RAxML/ASTRAL analysis have been performed also without C. consors. From the results, it does not seem to be the case, but if the authors decide to keep C. consors in the dataset, it would have been interesting to perform the same type of tree reconstructions to make them comparable.
Results: even if the focus is on Patellogastropoda, it would have been nice to have a short statement about the rest of the tree, e.g. “the relationships of the other classes remain unchanged whatever the % of missing data (Caeno+Hetero, Veti+Neomph), only the Patellogastropoda position is affected”.
L158: the expression “With more species missing” used here and elsewhere can be misleading, and supposes that a whole species is missing, while it means that for each SOG, one species can be missing. I would write “with more species missing per locus”.
L178: I understand that the authors wanted to be able to compare their trees with Chen et al’s tree, but this is at the cost of using a more recent and complete dataset. The goal of the manuscript is to test the effect of missing data on the topology, and this is achieved with the four datasets used by the authors, and the comparison with Chen et al’s tree does not add a lot to the point.
L185: “High-quality”: some of the used genomes are not really of “high quality”, in particular C. consors.
L192-193: I fully agree, but again I am not convinced that it has been done properly here…
L200: “highest posterior probability”: do you mean the PP of the whole tree? Of the average PP of all the nodes?
L205-206: Lautoconus ventricosus is even better…
L221: it would be nice here to indicate the number of genes used by Sun et al and Lan et al.
Table 1, Column header: SOG instead of SCOG.


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: HOW MANY SINGLE-COPY ORTHOLOGOUS GENES FROM WHOLE GENOMES REVEAL DEEP GASTROPOD RELATIONSHIPS?
Review round: 2
Reviewer: 1

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


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

Input:
Title: MIR-34A-5P INHIBITS THE MALIGNANT PROGRESSION OF KSHV-INFECTED SH-SY5Y CELLS BY TARGETING C-FOS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled “Study of miR-34a-5p inhibiting the malignant progression of KSHV-infected SH-SY5Y cells by targeting c-fos” by Shuyuan Wu et al. investigated the effects of miR-34a-5p on growth and motility of SH-SY5Y cells infected with Kaposi's sarcoma−associated herpesvirus (KSHV) by regulating c-fos.
Experimental design: 1.	The study lacks a control of miR-34a-5p-depleted SH-SY5Y cells. Can miR-34a-5p knockdown transform uninfected SH-SY5Y cells and increase cell growth and migration?
2.	What is the sequence of c-fos 3-UTR-mut in Figure 4A?
3.	The statistical method used in Figure 4B is improper. One-way ANOVA should be used to test whether it is statistically different among all compared groups. Multiple comparison is followed to test which two groups are different.
4.	Figure 4C did not show the correlation between c-fos mRNA level and miR-34a-5p, as stated. To prove correlation, authors need to calculate correlation coefficient.
5.	In Figure 7, mRNA expression data of each gene should be presented in the same panel. Therefore, panel A and B, panel C and D, panel E and F, and panel G and H should be in the same panel. It is expected that overexpression of miR-34a-5p inhibits KSHV genes.
Validity of the findings: Authors well characterized the phenotypes of SK-RG cells. Major phenotypes that were affected by miR-34a-5p should be reproduced and validated in a second neuronal cell line.
Additional comments: The manuscript will be improved by moderate English editing.


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: MIR-34A-5P INHIBITS THE MALIGNANT PROGRESSION OF KSHV-INFECTED SH-SY5Y CELLS BY TARGETING C-FOS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, Wu et al aim to investigate the role of miR-34a-5p on the proliferation and migration of KSHV-infected SH-SY5Y cells and study how miR-34a-5p regulates c-fos. They found miR-34a-5p was decreased in SK-RG (KSHV-infected SH-SY5Y) cells. Increasing miR-34a-5p in SK-RG cells reduced its proliferation, migration, which could be associated with decrease of CDKs and MMPs. In addition, overexpression of c-fos (one target of miR-34a-5p) restored miR-34a-5p mimic-mediated decrease of proliferation, migration, CDKs, MMPs, and KSHV gene expression. In vivo, miR-34a-5p agomir reduced tumor formation. Generally speaking, this study is well-organized and well-designed. Following are the comments:
1. Language editing is needed. The grammatical errors significantly decreased the accuracy of the information that the authors wanted to deliver.
2. I have concern about the efficiency of rKSHV.219 infection. From Figure 1A, the successfully infected cells should carry GFP. However, from their data, the infection efficiency is not 100%. In this case, sorting the GFP positive cells is needed. Otherwise, wild type SH-SY5Y cells will be mixed into the SK-RG cells. Thus, the results will be less reliable.
3. The authors should at least label out the most upregulated and downregulated miRNAs in their volcano plot. Otherwise, why bother to show it?
4. I see under subhead 3.2 the authors wanted to study cell cycle. Then, cell cycle analysis would be recommended. Evidence directly shows that increase of miR-34a-5p leads to cell cycle arrest is needed.
5. Another issue of this study is the protein changes in western blot are not significant enough to convince people that those proteins were truly increased or decreased. This happened in Figure 3E-F, Figure 5F, and Figure 6E.
6. Did the authors run a power analysis to confirm the number of mice they needed for each treatment for their xenograft model?
7. Have the authors compared the c-fos expression in their SH-SY5Y and SK-RG cells? This is important.
8. It is unknow the regulatory pattern of miR-34a-5p, c-fos, and KSHV. Does miR-34a-5p regulates KSHV directly or the regulation is via c-fos? Further data are needed to clarify this.
Experimental design: Additional experiments are needed.
Validity of the findings: Most of the findings are sound.
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: MIR-34A-5P INHIBITS THE MALIGNANT PROGRESSION OF KSHV-INFECTED SH-SY5Y CELLS BY TARGETING C-FOS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have successfully responded to my comments.
Experimental design: None.
Validity of the findings: None.
Additional comments: None.


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: MIR-34A-5P INHIBITS THE MALIGNANT PROGRESSION OF KSHV-INFECTED SH-SY5Y CELLS BY TARGETING C-FOS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors improved their manuscript according to my comments. Now, there is just one issue remains. They did a cell cycle analysis according to my suggestion, which is good. However, from the FACS histogram, the change between two compared groups is marginal. Usually, FACS analysis software is capable of automatically labeling the frequency for each cell cycle phase. I would suggest the authors add the automatically generated frequency to their FACS plot. This will only make their data more convincing.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript presents several formatting errors, a missing reference, and some omissions in the citation format, as well as typos and lack of standardization in the use of symbols.
The introduction requires more work. For example, the last paragraph uses very general and broad ideas at the beginning and ends up being very specific. A better introduction can be seen in Sola-Ojo et al. 2021
The map requires more descriptive geographic and political information.
Haplotypes networks and phylogenetic trees need more informative labels and colors for haplotypes and specimens.
The conclusion is misinterpreting the important result of the absence of population structure found in the data.
The Acknowledgements paragraph is unclear.
Experimental design: The research question in this manuscript has been established in previously published articles (Adeola et al., 2020; Sola-Ojo et al., 2021). The new data verified the previous findings. However, the in-depth analysis of how the gene flow (direction and degree) reduces the population structure of this species within the country is still lacking. Demographic models (e.g., isolation-with-migration models, IM) can be a good alternative.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting genetic study of the Muscovy duck in Nigeria that despite their economic importance little is known about the genetic characterization of their domestic populations in the country. This study could provide valuable breeding material for the poultry industry in Nigeria and other countries in the world.

My main criticisms are:
1. Introduction: This section needs to expand the information about what is already known about population genetic analysis this species in other regions and the potential explanation of such pattern. The introduction highlight the importance of the CYTB gene, but not of the CYP2U1 gene. What are the expectations based on previous findings? Also, what is the intention of comparing samples of Nigeria with samples from India?

2. Methods: The objective of this study state that authors intend to evaluate different Muscovy duck populations from Nigeria and India, however detailed information about such comparison is not clear. Locations from India are not even shown in this section. Based on the Table 2, I uderstand that the authors only cited results from a previous published study of Muscovy duck populations from India, but are not part of the analysis of this paper. The information here has to be better clarified.

3. Results: Figures needs to be improved in terms of design, resolution and size. The map lacks critical geographic information (latitude, longitude, scale, geographic reference, etc.). Color patterns and labels shown in the map and haplotype networks are not easy to understand.

3. Discussion: Authors provide hypothesis about unrestricted gene flow between populations, but no analysis regarding this aspect has been analyzed in this study. I would suggest to include isolation-with-migration (IM) models in the analysis, since they include parameters for population size, time of population separation, and gene exchange between populations. Such analysis can also provide more information for proper discussion of demographic aspects in this study.
Experimental design: The experimental design shown in the methods does not properly align with the objective stated in the introduction. A better organization of the information has to be done.
Validity of the findings: I have no comments on this section.
Additional comments: I have no comments on this section.


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors reported a paper on genetic diversity and population structure of muscovy duck from Nigeria.
The topic of the work is interesting and focused on the genetic characterization of local breeds/populations. However, there are some points of concern to be clarified and that make the paper not acceptable in the present form.
General comments about the introduction section:
-please try to furnish some more information about the current census of this breed in Nigeria. If number of heads is not available also the number of farms could be useful.
-lines 63-64: the authors wrote that the previous studies about genetic characterization are insufficient. Please try to summarize the main findings of the previous studies in this section (in few lines), just to present the state of art.
-line 65, the authors cited the "conservation of this breed": if I understood well is not endangered in Nigeria, is it? Please clarify this aspect.
No information in the introduction section are reported about the CYP2U1 gene: this is a major weakness. Please try to supply information that can justify the use of this marker.
Experimental design: I have a major comment about the aim of the work: why the authors included samples from India in their study? Is there any ethnological reason? Any evolutive reason? As the authors correctly reported the origin of this breed is from Central and South America. This aspect should be very well explained, otherwise the inclusion of samples from India is not justified.
Specific comments:
-line 94: please specify how many males and females.
-line 98: if the authors collected 2 samples per flock the final number of samples should be even...
-lines 99-100: it is quite strange to maintain the FTA cards in ethanol or stored at -80°C. Usually the FTA cards are stored at room temperature.... Just a comment.
-line 105: please specify the percentage of agarose used to prepare the gel. Moreover, please supply Nanodrop technical information (model and company).
-line 129: for what reason the number of sequences among the two markers is different?
-line 134: it could be better to specify how many sequences from India and how many from Nigeria.
-line 138: please supply a reference for MEGA software.
-line 143: please add a dot at the end of the sentence.
Validity of the findings: Results section
Please be consistent in using acronyms and abbreviations, i.e.:
-lines 183 and 184: Hap_4 and Hap_8 but in lines 202 and 203 HT4 and HT8
-Fst is written correctly in line 217. Please revise this acronym in all the manuscript long (including tables).
-line 193: please clarify why the authors used the chicken sequence to root the pylogenetic tree.
-lines 240-243: this part could be moved to materials and methods section.
-line 329: be careful in speculate bottleneck effect: no bottleneck analysis was carried out in this study.
Additional comments: No additional comments


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: There are still several inconsistencies or mistakes in data and table formatting.

Figure 1
The information of the number of samples by locality from the previous first draft was good. I suggest bringing that back.
Even though Niger and Kwara are published data it is good to have those localities on the map.
An inset map, an overview of the main map, including Nigeria and India could be a good option to provide a better overview of the main map.

Table 1, Table S1 and S2
The number of samples (Size1) for table 1, S1, and S2 of Ekiti and Kwara is different for the haplotype ADE15

Table S1 and S2 CYTB haplotype
There is inconsistency in the formatting of the tables. The column headings use capitalize and non capitalized names. Also, the "Frequency" label is different. Some values are centered and in bold. The same looks like are happening with Table S3 and S4.
Experimental design: No comment
Validity of the findings: Expand the idea of "human activities" in the discussion and conclusion.
This probably is the most important process in the lack of genetic structure in this domesticated species.
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: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article has been significantly improved, although I have a few observations. Attached my general/specific comments:

1. Introduction: Even though authors highlighted the importance of the CYTB gene and CYP2U1 gene, authors mentioned an additional marker (mithocondrial D-loop) that is not even explored in this article.

Lines 91-92: Why is it relevant to mention the areas of expression of the CYP2U gene at the organs level in the article? If it is worth to mention, you should do the same for the other markers.

2. Discussion: There seems to be a misinterpretation of the regression analysis results when authors mention that there is a "significative negative relationship" between genetic and geographical distance on the two genes. Make sure you consider the slope value and the range of genetic distance into account in your discussion of this aspect.

3. Figures: Map in Fig 1 still has to be improved. Please have an inset of Africa to show where the sampling sites are at a large scale. Also, make sure you include critical geographic information (latitude, longitude, spatial reference system). Change the symbol shape of locations shown in the legends for Fig S1 and S2; use a circle shape instead of a pentagon.
Experimental design: I have no comments on this section.
Validity of the findings: I have no comments on this section.
Additional comments: I have no comments on this section.


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 2
Reviewer: 3

Output:
Basic reporting: First of all I want to thanks the authors for their efforts in preparing this revised version that in my opinion is more understandable for the readers.
Experimental design: It is now well explained and complete.
Validity of the findings: The authors modified the manuscript according the reviewer's comments and the new version is improved and acceptable in the present form.
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: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 3
Reviewer: 1

Output:
Basic reporting: Very good job improving the manuscript. I don't have any major concerns with it.
A few simple observations are marked in the annotated manuscript.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: GENETIC DIVERSITY AND POPULATION STRUCTURE OF MUSCOVY DUCK (CAIRINA MOSCHATA) FROM NIGERIA
Review round: 3
Reviewer: 2

Output:
Basic reporting: I have no comments. I would like to acknowledge the authors for their efforts improving the manuscript.
Experimental design: I have no comments. I would like to acknowledge the authors for their efforts improving the manuscript.
Validity of the findings: I have no comments. I would like to acknowledge the authors for their efforts improving the manuscript.
Additional comments: I have no comments. I would like to acknowledge the authors for their efforts improving 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: THE POTENCY OF MINERALS TO REDUCE ORIENTAL FRUIT FLY INFESTATION IN CHILI FRUITS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: Line 25: damage

Line 29: Semi field I would refer to these at Semi field bioassays or cage bioassay throughout the manuscript.

Line 31: untreated control

Line 124-126: In the interest of reproducibility could sources of the minerals be included also?

Line 129-131: Did the control consist of a mixture of the wetting agent (Sodium Lauryl Sulfate) and the dispersant agent (Sodium Naphthalene Sulfonate formaldehyde condensates) or was it just water?

Line 171 - 172: What test was used to test normality and the homogeneity of variance?

Line 307 - 309: Great point!


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 POTENCY OF MINERALS TO REDUCE ORIENTAL FRUIT FLY INFESTATION IN CHILI FRUITS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript presents a study on response of fruit flies towards some minerals. The study is overall interesting and it will contribute to reinforce the valuable use of minerals in insect pest management. However, the work is poorly presented and not at all well described.
Introduction section is unnecessary long. Content presented in lines 53-62 is not required. The English language should be improved to ensure that an international audience can clearly understand your text (for example: line 102 is not clear). I recommend to ask an English native speaker to check the manuscript.  It is better to mention the innovation of the study clearly.Figures and table have not labelled and described appropriately. Methods have not described with sufficient detail and information to replicate.
Experimental design: Original primary research within Aims and Scope of the journal.

Figures and table have not labelled and described appropriately. Methods have not described with sufficient detail and information to replicate.

Rigorous investigation performed to an ethical standard.
Validity of the findings: Impact and novelty not assessed. It is better to mention the innovation of the study clearly.

All underlying data have been provided; they are robust, statistically sound, & controlled.

Conclusions are well stated, linked to the original research question & limited to supporting results.
Additional comments: Some questions:
-Is chili correct? Based on some references like (Votava et al., 2005), I found chile for (Capsicum annuum var. annuum L.).
•	Votava, Baral, and Bosland. 2005. Genetic diversity of Chile (Capsicum annuum var. annuum L.) landraces from Northern New mexico, Colorado, and Mexico. Economic Botany, 59, 8–17.
- Line 127-You dried all minerals at 60 °C for 14 hours. Why 14 hours? I could not find a reference in your manuscript.
- Line 138- In materials and methods section, you mentioned that twenty chilies were dipped in the mineral suspension with the concentration of 2% (W/V)? Why did you choose this concentration?
- Lines 139 and 161- You applied water as control and used minerals+wetting and dispersant agents for treatments. How to prove that efficacy in treatments is solely due to just minerals, and wetting and dispersant agents have no lethal effect?
-The titles of figures and table are not well described and should improve them. For example:
Average number of fruit fly visits on chili fruits (x̅ ± SE) ---> Average (x̅ ± SE) number of fruit fly visits on chili fruits treated with some minerals 24 hours after treatment under lab conditions.
Minor comments:
Line 29: in laboratory and in semi field ---> under laboratory and semi-field conditions
Line 31: in laboratory ---> under laboratory conditions
Line 46: Paticle film????
Line 50: Bactrocera dorsalis (Hendel) ---> Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)
Line 65: one of important ---> one of the important
Line 83: Mediterranean ---> mediterranean
Line 84: Ceratitis capitata (Wiedemann) ---> Ceratitis capitata (Wiedemann) (Diptera: Tephritidae)
Line 88: spotted wing drosophila fruit fly Drosophila suzukii ---> spotted wing drosophila fruit fly, Drosophila suzukii
Line 91: boll weevil Anthonomus grandis---> boll weevil, Anthonomus grandis
Line 138: Twenty chili fruits??
Line 152: Semi field study---> Semi-field test
Lines 187, 192, 198, 200: Control---> control
Line 221: In the the ---> In the
Line 223: in laboratory and semi filed---> under laboratory and semi-field conditions
Line 243: efective ---> effective
Line 244: adult bean weevils ---> adult of bean weevils,
Line 256: calcium hydroxida ---> calcium hydroxide
Line 279: kondirion???
Line 295: It (Driggers, 1929) is a very old reference. Was there no newer reference?
Line 309: You suggested the application of calcium hydroxide, calcium oxide or calcium carbonate at the concentration of 2% need to be integrated with other control methods. I would like to know which methods?


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 POTENCY OF MINERALS TO REDUCE ORIENTAL FRUIT FLY INFESTATION IN CHILI FRUITS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Comments to the authors
The manuscript is interesting and   have some merit   but before  accepting  it for publication  the following  issues need to be addressed:

1 – There are some typo graphical errors  that need to be corrected eg  in  line 73,  279  etc
2- The English language should be improved ,. Some examples where the language could be improved include lines 65, 71-73 , 134- ,178,the sentences should be properly rephrased  for clarity
3. On the materials and methods- . The study location should be properly described on the first
    paragraph .
- The name of the laboratory  used for this study should be stated
- The laboratory conditions where the experiment was conducted should be clearly stated.
- Which type of sugar was used in feeding the adult fly?  Specify.
-What percentage of sugar solution or quantity of sugar was used in feeding the
   adult oriental fruit fly? Please specify
-The sources of minerals used must be clearly stated
. The author stated that he/she used Randomized Block Design in the laboratory study. -  - What was the blocking effect? CRD is mostly used for laboratory studies, if otherwise, clarify by stating the blocking effects used

4. The title of figures 1-3 should be rephrased and the figure title should be placed under the
     figure not above the figure
 5. Authors should further provide proof that the used minerals are safe to man and environment
     on the discussion section
Experimental design: The experimental design used for the laboratory studies need to be  cross checked  and justified if otherwise .
Validity of the findings: The findings are valid
Additional comments: No further 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 POTENCY OF MINERALS TO REDUCE ORIENTAL FRUIT FLY INFESTATION IN CHILI FRUITS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Literature references, sufficient field background/context provided.
Professional article structure, figures, tables. Raw data shared.
Self-contained with relevant results to hypotheses.
Clear and unambiguous, professional English used throughout.
Experimental design: Original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Methods described with sufficient detail & information to replicate.
Validity of the findings: All underlying data have been provided;
Conclusions are well stated, linked to original research question & limited to supporting results.
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 POTENCY OF MINERALS TO REDUCE ORIENTAL FRUIT FLY INFESTATION IN CHILI FRUITS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors have made zealous efforts to revised the manuscripts based on the comments raised by the reviewers  , however, I still observed minor errors that hat to be corrected before final publication of this manuscript
1. The two sentences in line 58 -59 should be combined as one sentence as ''These control techniques however, have limit as fruit  fly trap still relies on the use of the male attractant (methyl  eugenol)." not as written as two sentences.
 2. In lines 122-126.  authors tried to address the sources of the minerals as raised  by putting it in the bracket. That indicated another meaning entirely. Since the ten minerals used were sourced from different places, It will be better to put in a tabular form  to avoid clumsiness in describing the sources of each minerals  in sentence form. The idea of putting it  in  bracket is out of place and it meant something else not what they intend to achieve.
Experimental design: OKAY
Validity of the findings: Valid
Additional comments: The manuscript should be considered for publication after the minor correction  raised


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: ELOVL2-AS1 INHIBITS MIGRATION OF TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: - I find this manuscript well-written and easy to follow. I would like to suggest raw data should be cited in the text. I saw you attached these files in the figshare platform, but you can add some text mentioning these links.

- Regarding figure organization, I think you can include the figure FC in the conventional numbering of the article.
Experimental design: - I think the design follows the hypothesis showing interesting results for proposing the ELOVL2-AS1 region for further analysis.
Validity of the findings: - Taking together the figures in the text and supplementary, the results seem valid to answer the hypothesis. No more 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: ELOVL2-AS1 INHIBITS MIGRATION OF TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors here report ELOVL2-ASI as a potential prognostic biomarker for TNBC. They identified key enhancer region in breast cancer by applying integrated analysis.
The overall paper is very well written with clear language.
The references are mentioned wherever is needed. However, it would be helpful to mention reference in line 217 to 220.
Figures, tables and raw data are well described.
Experimental design: The overall experiment is very well design. From data extraction, eRNA analysis to cell assays support the hypotheses. Controls are included wherever necessary. It would be interesting to know how many MDA-MB-231 cells were used for lentivirus infection.
Validity of the findings: The data provided by the authors is sufficient to support the hypotheses. The results are very well explained and clearly stated. The data presented is supported by sound statistics.

The conclusions are clearly stated and connected to the original research question.
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: ELOVL2-AS1 INHIBITS MIGRATION OF TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is an interesting manuscript that the authors have taken good use of several bioinformatics tools to identify a research target and explore its functions and possible regulatory mechanisms. This reviewer enjoyed reading it and would like to a few suggestions.
Experimental design: To better support that ELOVL2-AS1 could be used as a therapeutic and its regulatory relationship with ELOVL2, the authors may consider a ELOVL2-AS1 knockdown assay (if possible) see how that affects expression of ELOVL2 and BRCA cell migration.
Validity of the findings: The expression of ELOVL2-AS1 in the OE cell is dramatically different from that of the control, will this  affect cell viability and physiology characters?
Additional comments: The authors should provide information on sample size and number of repeats in each assay in the method part as well as in figure legends and/or figures.
The resolution of figure 4,  5 (A) and (C) and figure S2 needs to be improved.


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: ELOVL2-AS1 INHIBITS MIGRATION OF TRIPLE NEGATIVE BREAST CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: Dear authors,

I think the manuscript is well-written and easy to follow. Also, you have answered my minor concerns suffice. Therefore, I recommend this manuscript for its 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: WHOLE MITOCHONDRIAL GENOME SEQUENCING OF MALAYSIAN PATIENTS WITH CARDIOMYOPATHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: English should be improved
•	Examples:
•	The findings of this study are crucial to shed light on the distribution of mitochondrial mutations in the Malaysian CMP patients
•	HCM is characterised by left ventricular hypertrophy due 48 to cardiomyocyte hypertrophy and DCM is characterised by enlarged cardiac chambers and 49
                The exact aetiology of CMP remains 53 inconclusive. It is generally accepted that environmental and genetic factors play a vital role in the 54 onset of CMP
385 Besides, it was also not rare to find reported defects and deficiency in Complex III, especially 386 MT-CYB (Hagen et al. 2013a) and Complex IV
Genetic defect in MT-tRNA and MT-rRNA  adversely affect the transcription, translation and synthesis of mitochondrial protein…….
Comment2
The figure :Heatmap of conservation index (CI) and pathogenicity of variants predicted by in-silico tools should be more clear and readable
Experimental design: Comment1
You restate that the identified variants are pathogenic. I would, however, state that you have not undertaken mitochondrial genetics studies in their mother and siblings, and.  In studied patients parents were examined??, but there were no explanations/data about parents. More information about the genotype of parents should be added
« except m.9804G>A that was heteroplasmic with 21.4% load (sporadic inherited ??)
Comment2
There was no description of a control group for MC sample in Methods and Materials.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: WHOLE MITOCHONDRIAL GENOME SEQUENCING OF MALAYSIAN PATIENTS WITH CARDIOMYOPATHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The introduction gives sufficient background into the study. In the methods, it is unclear as to whether these patients have had the nuclear encoded genes associated with cardiomyopathy sequenced such as sarcomeric gene - if this has or hasn't occurred it should be clearly indicated.
The results section could be substantially modified to make it more clear and concise as only 207 of the 1077 need any discussion, I would re-mention Figure 1 indicating here where the variants were filtered out in the text and why, for example 'we performed a multi-step filtering procedure as illustrated in Figure 1. In the first step X variants with a global allele frequency of X% were removed etc'.  The three novel synonymous variants do not need mentioning either. The section on haplotypes could also be shortened especially with the inclusion of this data within the figure 1 filtering protocol.
Table 3 and 4 contain too much unnecessary information, at least 13 of the variants presented are haplotype-related or clearly polymorphisms.
Discussion sections of this manuscript could be made more concise.
Experimental design: The analysis of novel variants for pathogenicity lacked rigour. The selection of species included within the conservation index for evaluation of protein coding genes was not appropriate. All species included were primates, for this analysis to be performed correctly a selection of at least 10 diverse species from humans, primates, marsupials, mammals, birds, fish, insects and yeast should be used. A CI score of 10 or greater is considered highly conserved, and 8 or greater conserved, any less than 8 is not considered conserved. For analysis of tRNA variants, the structural significance of position, base pairing and the conservation of the nucleotide should be investigated using MitoMaster, MitoTIP and Mamit-tRNA (http://mamit-trna.u-strasbg.fr/).

In the discussion, there was no mention of the alternate change at m.8573 which is reported in ClinVar as benign. The Serine residue disrupted by the m.11918T>G variant is only conserved down to mammals and the conservation index calculated in this paper artificially inflates the importance of the serine. All CI's of novel variants need to be recalculated.
Validity of the findings: The conclusions about complex I being the most common complex which possessed disease-associated variants is untrue, firstly these variants have not been shown to be disease-associated and is most likely due to the fact that complex I contains the most number of mitochondrial encoded subunits and chance.
The authors should take into consideration the levels of heteroplasmy/homoplasmy in tested tissues can also be vastly different to affected tissues, some variants such as the m.11778G>A variant can also have decreased heteroplasmy in blood with age and also show incomplete penetrance within families.
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: PRE-COMPETITION MENTAL ENERGY AND PERFORMANCE RELATIONSHIPS AMONG PHYSICALLY DISABLED TABLE TENNIS PLAYERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: An interesting article that was generally well written that investigated relationships between the concept of energy and performance.

The work has value to the sports psychology community and the concept of energy as the authors indicate is one that has not been researched a great deal. However, I would like the authors to expand the literature and provide greater conceptual clarity for how energy links with existing concepts such as mood, emotion, self efficacy etc. It appears they are introducing a relatively new concept and in doing so it would help if it's was conceptualised within the existing literature with greater clarity.
Experimental design: The article is original and within the scope of the journal.

The research question is suitably well described. The authors have provided some indication of how research identifies a gap in the literature.

The methods the authors have a strong degree of rigour.  However, I would like to see stronger justifications on when the measures were taken. For example why take measures of energy a day before competition rather than relatively close to performing?

The methods are suitably well defined and described to allow replication.
Validity of the findings: The authors could provide a stronger rationale for the data analysis methods chosen.

At present, they emphasise the significance of the results rather than the strength of relationships.

I would like to see some thought as to the mechanisms underlying hypothesise relationships, that is we know that energy links to performance but why should this be the case? with the subcomponents of the energy scale it might be possible to set an test hypotheses.
Additional comments: Definition of energy warrants greater focus. at present the consequences of energy are part of the definition. If someone is displaying intense concentration does this therefore mean that they are displaying intense energy?
This is debatable because it may be relatively easy for someone to concentrate and therefore intense energy is not necessary. This is just an example of where there is a definition where the consequences other constructs are not distinguish from the construct itself.

Martens (1987, p.49) suggested that if we know little about something in sport
83 psychology, the ideographic approach is an alternative way to gain knowledge. It would be useful to explain why this might be the case

Athletic Mental Energy Scale (AMES, Lu et al., 2018) one day before the competition and completed the self-referenced performance measure approximately one hour after the competition.

Authors should provide a justification for the temporal decisions in their study -for example why one day before competition? This is especially important as emotions and moods can vary from moment to moment and therefore they may have little bearing on mood states going into competition.


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: PRE-COMPETITION MENTAL ENERGY AND PERFORMANCE RELATIONSHIPS AMONG PHYSICALLY DISABLED TABLE TENNIS PLAYERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Many thanks for reviewing this manuscript Pre-competition mental energy and performance relationships among physically disabled table tennis players. The authors presented a test of the relationship between Pre-competition mental energy and athletes’ performance, by two studies from physically disabled table tennis players. The topic and research questions are novel and significant; however, I have several comments and suggestions that would need to be addressed before I can recommend publication. These are outlined below.

1. Insufficient review and discussion of relevant literature. While authors briefly introduced a relatively novel concept named mental energy in their study, they seemed not aware of much of the mental energy and its components-related literature and theories in psychology, sport, and performance domains. For example, as vigor, confidence, emotions, and other components can be regarded as psychological resources that have been linked to performance, using resource-based theoretical perspectives in sports and performance literature for developing hypotheses and justifying the psychological mechanism of mental energy and performance would provide more solid foundation and insights into their work. Specifically, I found the hypotheses development and the arguments mainly built on reporting past results instead of theoretical justifications, which is, to some degree, insufficient and not convincing. Here I suggest authors draw on literature/theory in sport psychology to provide a more comprehensive and complete theoretical reasoning for the relationship between mental energy and performance.

2. A lack of solid reasoning for the chosen subject. The authors have provided some good reasons for the important target of physically disabled table tennis players and why we should put more attention on them. However, the current reasoning mainly explains the background and current situation regarding participation in competitive sports as well as the benefits of engaging in competitive sports. It is advisable to provide more concise reasons to justify why physically disabled table tennis players would be the important target when investigating mental energy.
Experimental design: 3. Methodological concerns. Using two studies to test research hypotheses indeed provides more rigorous results. However, the sample size, in general, is too small to conduct statistical analysis, especially Pearson correlation and multiple regression. Although the reported results were significant as the authors’ expectation, these findings might be relatively unstable and unreliable, as a small sample size decreases the power of the study and enhance the margin of error. Moreover, the current statistical analysis was based on between-person analysis but not within-person analysis according to the analytic methods authors used. To further confirm the nested data structure of study 1, multilevel linear modeling would be necessary to adopt in the study; however, due to the small sample size, HLM is not suitable to use. Here I suggest the authors (1) increase the sample size, (2) pool the sample of study 1 and study 2, or (3) remove study 1.2. A lack of solid reasoning for the chosen subject. The authors have provided some good reasons for the important target of physically disabled table tennis players and why we should put more attention on them. However, the current reasoning mainly explains the background and current situation regarding participation in competitive sports as well as the benefits of engaging in competitive sports. It is advisable to provide more concise reasons to justify why physically disabled table tennis players would be the important target when investigating mental energy.
Validity of the findings: 4. Discussions here are more limited around the current results. It would be beneficial to have more consideration, conversation, and discussion of theoretical contribution (or at least broadening the discussion section) in the sport psychology literature (refer to the first point of comment).
Additional comments: Minor Comments
(1) L.110: It is advisable to report more complete demographic information (e.g., gender, weekly training hours…).
(2) L.217-220: Was the measure of performance collected by both subjective and objective data? If so, the authors might analyze both two indices to obtain more rigorous results.
(3) When the AMES was collected? Is it corresponding to the definition of pre-competition? The authors should clearly describe, define, and explain.
(4) It is advisable to add a table to display the regression results.
(5) L.232-233: “only confidence was selected into the model” Did authors actually use hierarchical regression? It seems that step-wise regression was employed but not hierarchical regression. However, using hierarchical regression would be more appropriate in explaining the theoretical implication, so I suggest authors reconfirm their data analytic approach.
(6) L.260-263: “Research in other domains such as nutrition science
suggested that intake of energetic supplements (e.g. Ginkgo biloba) improves mood and attention
in healthy subjects, and consuming omega-3 polyunsaturated fatty acids reduced the risk of
age-related cognitive decline (Gorby, Brownawell, & Falk, 2010).” This sentence seems irrelevant to this study and would be better removed or replace with other arguments.
(7) L.329: It is questionable that the authors mentioned “both studies adopted a longitudinal approach” as study 2 did not use repeated measures across time (i.e., study 2 adopted a time-lagged design).
(8) L.345: Why authors merely recommend future research to focus on strenuous sports? Is there any reason that researchers should put more attention to this type of sport? What about team sports? It would be better to explain more about this idea.


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: PRE-COMPETITION MENTAL ENERGY AND PERFORMANCE RELATIONSHIPS AMONG PHYSICALLY DISABLED TABLE TENNIS PLAYERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This revision has improved the paper, theoretically and empirically. I appreciated that attention to detail. I advocate there are some further refinements needed.
Experimental design: The contents and explanations are appropriate.
Validity of the findings: L.324-325: with respect to the use of hierarchical regression analysis, I suggest the sentence “only confidence was selected into the model…” should be revised because all the predictors were in the model and just one predictor was significant. Moreover, for more comprehensive information to readers, it is advisable to report all the values of unstandardized or standardized coefficients of all predictors in Table 5.
Additional comments: The notes of significance in Table 2 to Table 5 need to be corrected. It is “*p < .05, **p < .01” but not “*P>.05,**P>.10”.


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: FIRST DNA BARCODE LIBRARY FOR THE ICHTHYOFAUNA OF THE JOS PLATEAU (NIGERIA) WITH COMMENTS ON POTENTIAL UNDESCRIBED FISH SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: After carefully reading the manuscript, I found many small typographical errors and few sentences that were not clear and of difficult comphrehension. I added in the revised PDF, comments and suggestions on how o improve it.

The structure of the Introduction can be improved. I suggested some paragraph reorganization, making a a first block directed to the description of the Jos Plateau and a second block about its fish diversity. Previously, some parts of the text focused on the fish then it was followed by an abrupt change to the physical description of the Plateau and going back to the fish and to the Plateau again. My suggestions (on the PDF) is only one idea on how the authors can improve that section.

Two Supplementary tables contained minor typographical erros, and I am also attaching to this review (Supplementary files 9 and 11, table 2and 4, respectively). Also, I could not find any caption for the supplementary figures 2, 3 and 4, and I also noted that for some of the specimens (differentiated by letters) the scale bar is missing. These are: Supplementary figure 2, letter b; supplementary figure 3, letter e; supplementary figure 4, letter f.

All the genera authorships are between parenthesis, but this should not be the case. Please revise all the manuscript.

The Map figure need to be improved. I could barely see the river names (in grey), and also I could not have any idea of which rivers flow into each of the three main watersheds in the region, the Benue, the Niger and the Chad. In a next version of the map, I expect to see at least a small map, showing the three main watersheds, where the Jos plateau is located, and the watershed divides (maybe hashed lines).
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear Authors,

It was really nice to see that there are ongoing research related to the fish diversity in the Jos Plateau, a region with not many species, but as suggested by the results, a really heterogenic fauna, sharing close affinities with other African ichthyoprovinces. The article is straigthforward and the conclusions take into account the limitation due to the use of only one marker (COI). It is a great contribution for future fish surveys in west Africa and a nice model to be followed by other similar research in Africa.

As I mentioned in the Basic reporting section, there are many small issues, related to the writting, some corrections that need to be done in the supplementary files and the main issue in my point of view is the map. The map is not clear and need many improvements.

Given the commens I made, I consider that the paper should go through minor revision.

Sincerely,

Pedro Bragança


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: FIRST DNA BARCODE LIBRARY FOR THE ICHTHYOFAUNA OF THE JOS PLATEAU (NIGERIA) WITH COMMENTS ON POTENTIAL UNDESCRIBED FISH SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no commentThe
Experimental design: no comment
Validity of the findings: The study has impact and novelty. All data is provided and is technically sound. Also the conclusions are well stated. This work represent a great contribution to discover an unknown biodiversity in a few studied area. Only, I would have liked to read more discussion about Coptodon morphs related only in results.
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: FIRST DNA BARCODE LIBRARY FOR THE ICHTHYOFAUNA OF THE JOS PLATEAU (NIGERIA) WITH COMMENTS ON POTENTIAL UNDESCRIBED FISH SPECIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper adresses the ichtyofauna of an understudied region in Nigeria. It provides an overview of this fauna with molecular data, and voucher specimens. The data is available publicly in BOLD and contains the required info and additional useful data. Export and collect permit were provided although I cannot judge whether they completely fulfill the legal requirements. The paper is generally clear and well written, although there are a number of mistakes to correct (image references and others) and clarifications to be provided, especially in the figures. The number of species is low, but the number of specimens is appropriate and in line with other barcode studies.
The discussion of the new potential species needs to be clarified and criticized on the characters (coloration for Clarias, etc.)

- The map is crucial for this publication, yet it lacks some of the relevant information. The color contrast between rivers and surrounding areas is not very legible, and should be ameliorated.
Ichtyological diversity is often structured according to basins, and the rivers from the plateau drain in several different basins. A clear distinction on the sampling map of the different basins (for instance with different color dots), as well as waterfalls and other obstacles to fish circulation would be needed. Also add the numbers from table 8 on the points (most are clearly distinct, the rest could be indicated with arrows). All these would help strongly with the discussion on waterfalls and sampling points.
- Please add the corresponding collection point numbers on fig 2 for each picture
- L209 if there was hybridisation, you would not observe distinct clusters. Hybridisation cannot make mitochondrial sequences closer to each other, so another hypothesis is needed
The supplementary figures are numbered differently in the text and the files (5, 6, 7 in the files and 2D, G… in the text), and the one for Labeo is missing

Identification: what were the complicated cases ? Please list them

Table 4 the 3 last columns are not very interesting, as they indicate the closest species in the dataset. This distance and species are really not representative of the interspecific divergence of the species with their closest neighbour (absent from the datasets). This should be replaced by the closest species in BOLD and divergence values from them.
Experimental design: Sampling level of completeness should be discussed, considering the low number of species.
Validity of the findings: See above
Additional comments: L45 Fundulopanchax gardneri nigerianus is widely present in the aquarium trade.
L56 , not ;
L66 tributary
rivers flowing south drain into the Benue River as well
L91 supplementary
part starting L113 please add the station numbers corresponding to the various categories
L116 on average ?
L156 Analysis
L161 Puillandre et al., 2012 is not the right reference for K2P on BOLD, or add following but they were not the first.
L200 the specimens you collected have low divergence, but the trees in additional data have higher divergence when including specimens from other locations.
L203 add the BIN numbers on the figure ?
L209 if there was hybridisation, you would not observe distinct clusters ? Hybridisation cannot make mitochondrial sequences closer to each other
L231 divergence with E. callipterus, and closest species in BOLD ?
L242 this is a NJ tree so cluster, not clade, and not optimal for relationships. For phylogenetic relationship discussions, maximum likelihood would be the right approach. For divergence NJ is fine
L251-253 where are the areas of collection for these species ? Same for the other closest species when not indicated (L257), it would be really valuable to have the info.
L341 how do you explain the low species number ?

Supplementary is written 3 different ways in the file titles.
Additional figure 7: Kalign not Kaling
Additional trees: it would be interesting to add indicate the corresponding localities next to the tree, to make them standalone,


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: FIRST DNA BARCODE LIBRARY FOR THE ICHTHYOFAUNA OF THE JOS PLATEAU (NIGERIA) WITH COMMENTS ON POTENTIAL UNDESCRIBED FISH SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Dear Authors,

After carefully reading the new version and reading the reply letter I am happy to indicate the paper to a minor revision section, not depending on a third review round.

I found only minor problems, most of them are: (1) the indiscrimate use of extra-paragraphs, not following a pattern; (2) genera name that are not in italic; (3) small gramatical errors. All the comments are provided in the attached PDF.

There is only one sentence that was not clear to me: Line 233 "Further.....". Please improve it.

I hope my suggestions were useful and contributed to the quality of the study.

Kind regards,

Pedro
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: FIRST DNA BARCODE LIBRARY FOR THE ICHTHYOFAUNA OF THE JOS PLATEAU (NIGERIA) WITH COMMENTS ON POTENTIAL UNDESCRIBED FISH SPECIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: This is a second review. The structure of the article was ameliorated.
Experimental design: Additional details were added where requested by the reviewers. Additional verifications have been made following the suggestions of the reviewers.
Validity of the findings: No comment
Additional comments: Most of the corrections requested by the reviewers were made, but a few new were introduced, including a number of uneeded parentheses around references.
There remains a number of more or less important problems. Is the inclusion of Figure 1 a mistake ? It is redundant with the much better, corrected map of figure 3.
In the additional figures, at least comment on the lack of scale for most of the sample. Is there no way to recover the scale from some detail in your pictures ?
In the introduction, there are double parentheses around several of the references.
L96 replace ; by ,
L130 eliminate this was
L131 first mention of the candidate species, unclear what they are, introduce them briefly. (« species that could not be identified » or something similar, or move the last paragraphe of this parts that introduces them before this phrase)
L133 when not if
L182 primers
L252 galilaeus
L259 hybridization with mitochondrial retention
L281, 287, and elsewhere : uneeded parentheses around references
L295 widely distributed
L215 and elsewhere : clade is not the appropriate term for a distance tree cluster, as already mentionned in the first review (cluster is just fine).
L334 group is needed, why bar it ?
L358 C. gabonensis is dispersed in distinct clusters, not regrouped together. But you cannot deduce polyphyly from a distance tree. It can look like semantics, but it is not, you would need a phylogenetic method for this (parsimony, ML, or bayesian inference).
L405 & 406 Garra


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: IDENTIFYING AND CHARACTERIZING STAGONOSPOROPSIS CUCURBITACEARUM CAUSING SPOT BLIGHT ON PINELLIA TERNATA IN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: -In general, clear and unambiguous, professional English is used throughout
-Literature references are adequate, but some of them are incomplete:
Guideline 184. Reference is not found in the literature
guidelines 189,191,194,209 and 234. References are incomplete. Missing authors
Guidelines 197, 200, and 203. References are not ordered by year.
-Professional article structure is correct. Description of the feet of the figure is poor. The microscopy images do not describe the staining techniques used in Figure 2.
Experimental design: Methods
Guidelines 85 to 87.
-The description of the methods is not clear.
-There is no complete information on the staining techniques used nor the amplification conditions of the PCR technique volumes of each reagent used are given, but not their concentrations.
Guideline 85.
-Primers are not well described. In the cited reference, they do not use the initiator LR5; they use LR7.
Vaghefi, N. and Pethybridge, S. J. and Ford, R. and Nicolas, M. E. and Crous, P. W. and Taylor, P. W. J. (2012) Stagonosporopsis spp. associated with ray blight disease of Asteraceae. Australasian Plant Pathology, 41 (6). pp. 675-686. ISSN 0815-3191
Methods are not sufficiently detailed for replicability
Results
Guideline 111.
-Fifteen fungi were isolated, 11 strains were the same organism (data not shown), and the other four were not results?
Guidelines 111 & 112
-describe one dominant strain? What characteristics of the AG-3 strain define it as dominant?
-In Materials and Methods, in the part of molecular identification of the fungus, in guideline 95, they say that they used Fusarium oxysporum as an external group in the phylogenetic tree, while in the results (Figure 3) in the phylogenetic tree, the fungus of the external group used is Alternaria brassicae.
Guideline 118.
-Have tiny oil droplets; how does it know? What staining technique did it use?
-There is no statistical analysis or results
-it is an interesting article because it describes for the first time the presence of the pathogen in the leaves of the plant, but the presentation of the results is more like a disease note.
Validity of the findings: -It is important to determine with precision the pathogenic fungus that is affecting the plant, in order to propose fungus control strategies, but it is not the only fungus they detect on the leaves of the plant.
-The 15 fungi that were isolated must have the same phenotype, and only one strain, AG-3, was analyzed, it is not clear why only strain AG-3 to used. Not discussed what happened with the other four strains.
Additional comments: the manuscript has errors in the description of the methods used and in the references cited that should be corrected.


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: IDENTIFYING AND CHARACTERIZING STAGONOSPOROPSIS CUCURBITACEARUM CAUSING SPOT BLIGHT ON PINELLIA TERNATA IN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is clearly written with a few editorial errors e.g. spacing issues. Specifically, some comments I have include:
Line 32 Add space before '(Thunb.)'
Line 38 Remove space between Chinese and Lung
Line 39 …to treat the symptoms of COVID-19
Line 72: Since this is the first mention of the isolate name (AG-3), it should be mentioned at this point that the pathogen was named AG-3.
Line 144: add space between S. and cucurbitacearum
Experimental design: Avoid repeating materials and methods in the Results section e.g.
Line 103-104: This statement should not be included on the results section
Validity of the findings: Line 111: Of the 15 fungal isolates, what were the other 4 that were different? This information should be included.

Brewer et al., 2015 provides PCR-based primer sequences useful for distinguishing 3 Stagonosporopsis species. Test these primers on AG-3 and the other 4 isolates to further confirm the S. cucurbitacearum bands and include that information on the manuscript.
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: IDENTIFYING AND CHARACTERIZING STAGONOSPOROPSIS CUCURBITACEARUM CAUSING SPOT BLIGHT ON PINELLIA TERNATA IN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Following the changes made by the authors, the manuscript is okay for publication.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: PIPECOV: A PIPELINE FOR SARS-COV-2 GENOME ASSEMBLY, ANNOTATION AND VARIANT IDENTIFICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: I reviewed with interest the manuscript entitled " PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification". PipeCov is a good example of intelligent and well-organized pipeline to assembly Sars-CoV-2 genomes, combining the advantages of using de novo and reference−based assembly strategies. As the authors demonstrate in detail throughout the manuscript, the use of these combined strategies allows to improve the assembly parameters with respect to the current reference assemblers for SARS-CoV-2. Another important aspect of PipeCov is it´s unique feature to have the pangolim automatically updated, eliminating the need to download new versions at each execution.
Experimental design: The methods are well documented and suitable for the present work
Validity of the findings: Minor comments:
Line 133 page 5. It seems like there are a couple of wrong characters (!,?)
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: PIPECOV: A PIPELINE FOR SARS-COV-2 GENOME ASSEMBLY, ANNOTATION AND VARIANT IDENTIFICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The PipeCov, a pipeline for SARS CoV-2 genome assembly, annotation, and variant identification, has an excellent approach for analyzing the novel coronavirus (SARS-CoV-2) with promising results. As they compare with other pipelines, they choose to use a "hybrid" approach with de novo and reference genome assemblies. They took advantage of these two procedures to minimize Ns' presence in the consensus sequences while maximizing the average coverage.
However, some issues need to be clarified to understand how the pipeline works.
Experimental design: About the methods, I missed the information about the default values of the pipeline. Honestly, are there any default values? I did not see it explicitly in the text. For example, what is the meaning of "low Phread score" (l.86) ? Which is the threshold of low quality and sequence length?
Yet, I do not understand the explanation in figure 1 how the "de novo" assembly with Spades connects with the reference genome of the Bowtie and Samtools. It seems this connection emerges by applying the script hcov_generate_consensus.R. I think it is worth a brief explanation of how it works despite the reference.
Validity of the findings: About the results, I am wondering why "120 amplicon datasets randomly extracted from 210 samples under "just one" Bioproject? Why not test in a few other Bioprojects? Another issue is how PipeCov keeps Pangolim automatically updated without downloading a new version at each execution?
Additional comments: In figure 5, the X axis is missing. It was not explained in the legend.


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: PIPECOV: A PIPELINE FOR SARS-COV-2 GENOME ASSEMBLY, ANNOTATION AND VARIANT IDENTIFICATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: First of all I suggest to review the english, spite of not being an english native person, I found some phrases a bit strange to interpret.
Then, I do not find the reason to promote the development of the pipeline. What is the problem that they intend to solve? Whay this is important? Why the reference and de-novo are required in this context? The emergence of the need is not clearly exposed.
The Table with sample details should be given as supplementary material and should be in english. It is not referenced on the text.
Experimental design: A section explaining the comparison process and used statistics as well as the rational of comparison procedures should be included in the methods section. The rational of the statistical methods should be provided.
For instance, results of figure 2 and 3 deserve some statistical test as well as to represent results as a boxplots to evaluate real differences between approaches.
Since the Briones et al 2020 is a technical and not peer reviewed manuscript. Spite that it can be ok, what they claim, I suggest that in this manuscript the quality rational should be stated as well as why the 1% Ns limits and the quality consensus and the explanation of the quality standards with appropriate discussion.

Figure 5, I do not understand the x-axis.
Validity of the findings: the novelty and needs for the development were not clearly exposed. Thus conclusions are weak.
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: PIPECOV: A PIPELINE FOR SARS-COV-2 GENOME ASSEMBLY, ANNOTATION AND VARIANT IDENTIFICATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The PipeCov, a pipeline for SARS CoV-2 genome assembly, annotation, and variant identification, has an excellent approach for analyzing the novel coronavirus (SARS-CoV-2) with promising results. As they compare with other pipelines, they choose to use a "hybrid" approach with de novo and reference genome assemblies. They took advantage of these two procedures to minimize Ns' presence in the consensus sequences while maximizing the average coverage.
After modifications, it is clear to understand how the pipeline works
Experimental design: Methods is described with enough details to understand the scope and the aims of the pipeline
Validity of the findings: The object of the pipeline is well stated. The results is promising  for the analysis of the virus SARS Cov-2 included those for de novo and reference genome.
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: PIPECOV: A PIPELINE FOR SARS-COV-2 GENOME ASSEMBLY, ANNOTATION AND VARIANT IDENTIFICATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been imrpoved, spite there are still some things that are not clear enouph for me.

Spite I consider that having good coverage is a desirable characteristic as well as having low Ns inserted in the genome, it seems that any of these advantage have an impact in variant discovery. The authors claimed that PipeCov will have a mayor impact on phylogeny analisis, but this is not demosntrated nor evaluated thus being just an hypothesis.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Minor revisions:
So, I thhink that a speed comparison should be included in order to evaluate the advantages of paying time efforts in the analysis if the intention is, for instance, to look for variants.

line 192:
"of N’s compared to the other pipelines. It is possible to no notice in Figure 3B that for some samples,"
i think that it should be

of N’s compared to the other pipelines. It is possible to notice in Figure 3B that for some samples,


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: SLEEP HEALTH OF AUSTRALIAN COMMUNITY TENNIS PLAYERS DURING THE COVID-19 LOCKDOWN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clear, unambiguous, used professional english throughout. In detail background is provided using references from literature. Article is structured, figures, tables and raw data is also shared.
Experimental design: It is a original piece of research within aims and scope of the journal. This research also stated how it fills an identified knowledge gap. rigorous investigation performed to a high technical and ethical standard. Methodology section was so clear with sufficient detail and information to replicate.
Validity of the findings: All underlying data have been provided, they are robust, statistically sound.

Conclusion needs a minor revision, it is just like a summary of the research. Conclusions should be supported by the results obtained not just the summary of findings.
Are the implications of the study identified?
Are there any recommendations for further research?
Does those recommendations identify how weaknesses in the study design could be avoided in future research?
Additional comments: comment 1 - In abstract, methods section would be better if authors can add study design and sample size.
comment 2 - only limitations of the study mentioned, that would be great if the strengths of the study is also provided.