PONE-D-25-06105Deciphering the Genetic Landscape of ToLCNDV: Dynamic and Region-Specific Diversity Revealed by Comprehensive AnalysesPLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1:  Dear Author

This MS was made based on totally online data available in GenBank, no original work.

Why this work was not done by using ToLCV sequences submitted from KSA?

All the data is used from GenBank and nothing new data in this MS, all are old.

In the introduction part, authors have mentioned that many countries but no KSA? Why?

In materials and methods section: From these datasets, sub-datasets were generated for each open reading frame (ORF). Additionally, sequences were categorized by country of origin, with further division into their respective ORFs to facilitate country-specific analyses. Where is KSA?

Results section: The figures and Tables: No data from KSA at all

Some figures are not with high resolution and should be replaced with high resolution fig.

The phylogenetic tree images are not at all visible.

Authors should provide the genetic diversity/similarity % in a table.

Figure 3. The phylogenetic dendrogram of selected sequences of ToLCNDV, TA (A) and TB (B), based on their respective full-length sequences. The phylogenetic tree was constructed with Maximum-Likelihood (ML) algorithm in MEGA11 with 1000 bootstrap values. Geographic origin (country) of the isolates is indicated by the coloured circle. Why not some sequences from KSA was used in this study?

RDP generates some important figures and data and this MS lacking those images.

Recombination breakpoints (start and end points) in ToLCNDV genome should be reflected in the image.

All the figures and Data is made and generated by softwares, there is no novel findings in this MS and does not reflect the originality of the work.

The accession numbers, name of the viruses’ acronyms are not available in this MS.

Discussion: This study used stratified random sampling to ensure each country was represented Proportionally to its population size, thus mitigating over- or under-representation.

Where is KSA data? If the funding agency from KSA then KSA data should be used so that the generated information will be valuable for KSA.

The generated data from this work is not as much as useful for scientific community as well as for KSA.

There are some grammatical errors were observed in the text.

Conclusion: Notably, Asian isolates displayed significantly, higher recombination rates, indicating location-dependent evolution. Again, KSA data missing.

Thanks

Reviewer #2:  I have critically reviewed the manuscript title “Deciphering the Genetic Landscape of ToLCNDV: Dynamic and Region-Specific Diversity Revealed by Comprehensive Analyses”, which describes the genetic diversity and evolutionary tracks of the most important tomato infecting bipartite begomovirus ToLCNDV. The manuscript is about very important issue of devastating begomoviruses which belong the largest genus of plant infecting viruses with wide host range. The manuscript utilized the advanced bioinformatics softwares to analyze the nucleotide mutation rate and recombination events in more than 650 virus complete genomes. The manuscript is well written describing the importance of study supported with update review of literature. Methodology of experiments are well explained to reproduce the experimental results. The results and discussions are comprehensively described. Although there are few typo errors which can corrected by careful reading of the manuscript.

I would recommend the acceptance of manuscript for publication in its present form.

Reviewer #3:  This paper studied “Deciphering the Genetic Landscape of ToLCNDV: Dynamic and Region-Specific Diversity Revealed by Comprehensive Analyses”. In general, this is a well written paper and the results support the main conclusion. Here, I would like to give few suggestions to further improve the manuscript:

1, The abstract can be more precise.

2, Briefly discuss how recombination may impact virulence, host adaptation, or resistance breakdown.

3, Briefly discuss why AC4 and Rep show diversifying selection while other genes are under purifying selection.

4, Emphasize the importance of integrated vector management (IVM) to limit viral spread.

Reviewer #4:  ToLCNDV is one of the important viral pathogens worldwide. Selection of problem is good. Manuscript is written nicely.

I have gone through the manuscript, the following corrections were raised and few highlighted in manuscript.

Quality of images of Fig 3 and Fig 4 should be improved.

Include all crops also and their distribution across the continents.

Include association of satellite molecules.

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Reviewer #1: No

Reviewer #2: Yes:  Dr. Khadim Hussain

Reviewer #3: No

Reviewer #4: No

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Deciphering the genetic landscape of tomato leaf curl New Delhi virus: Dynamic and region-specific diversity revealed by comprehensive sequence analyses

PONE-D-25-06105R1

Dear Dr. Iqbal,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

S.V. Ramesh, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #5: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #5: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #5: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #5: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #5: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #5: (No Response)

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If you choose “no”, your identity will remain anonymous but your review may still be made public.

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Reviewer #5: No

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