PONE-D-24-29673Comparative analysis of pattern-triggered and effector-triggered immunity gene expression in susceptible and tolerant cassava genotypes following begomovirus infectionPLOS ONE

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S.V. Ramesh, PhD

Academic Editor

PLOS 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: Yes

Reviewer #2: Partly

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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: Yes

Reviewer #2: No

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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: Yes

Reviewer #2: 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: The manuscript ‘Comparative analysis of pattern-triggered and effector-triggered immunity gene expression in susceptible and tolerant cassava genotypes following begomovirus infection’ [PONE-D-24-29673] is well-conceptualized, well-planned, and well-written. However, I have a few suggestions which could improve the manuscript.

Please provide key quantifiable results in the abstract section.

Line 14: ‘nearly a billion’ please quantify with the recent FAO database.

In the introduction, please mention various types of CMV and discuss the virulence of SACMV with SLCMV (Sri Lanka) and NDCMV (New Delhi).

Line 60: Please delete ‘2019)’

Line 117: MAMPs/PAMPs also induce Callose deposition, and cell death in leaves in addition to ROS. Please mention.

Line 172: In plant-virus interactions.. please delete ‘some’

The introduction seems to be incomplete/abruptly concluded. Please mention the future implications of the expected outcome.

Moreover, the authors have introduced challenge inoculation at 12, 32, and 67 dpi and mentioned 12 dpi as an early stage. Is 12 dpi an early event? I doubt the author will miss early events such as ROS, cell death/HR, and callose deposition at 12 dpi. Please justify.

Please mention ‘g/L’ as ‘g L-1’ throughout the text.

Line 189: Whether the nodal explants were virus-indexed?

Line 227: Please mention the date of access for the software used in the MS.

Line 238-239: Please mention the make, city, and country of the consumables/kits/equipment used in this study.

Line 244: Please mention H2O2 instead of ROS.

Please mention H2O2 as the section 2.4 and Transcriptional analysis as 2.5 followed by library preparation (2.6)

Line 256: Please write the full form of SMRT in its first appearance

Please keep the list of primers Table S2 and Table S1 in the main text.

Line 275,276, 278, 279: Please mention the date of access for the software used in the MS.

Line 298: Please mention the Caption after the figure. (For all figures)

Line 380: Please delete the word ‘Footnote’ from all the tables. Please write the footnote below the Tables.

Line 384: *P < 0.05 or *P ≤0.05?

Line 478: Please revise (Table 2))

Results and discussion are adequate

Please mention a line of future implications of the output in the conclusion.

Please cross-check the language, grammar, and punctuation.

Please cross-check the reference pattern as per the journal standard.

Line 688: 8. 0 References…please check the section numbering per journal pattern.

The number of references (86) may be reduced.

Please use high-resolution images in the Figures/graphs.

The manuscript is well-prepared per the journal standard and may be considered with minor revision.

Good luck with the revision.

Reviewer #2: The author discussed the physiological changes in plants when inoculated with South African cassava mosaic virus (SACMV) using susceptible and non-susceptible cassava varieties.

In particular, this paper discussed the plant immune response that occurs a mutual potentiation of cell membrane receptor-associated pattern-triggered immunity (PTI) and nucleotide leucine-rich repeat (NLR) effector-associated immunity (ETI) in plant immune responses when inoculated with SACMV.

It is interesting that the amplification process of SLCMV was investigated in detail at each day after inoculation, physiological investigations such as quantification of ROS were also conducted, and the discussion was performed from various perspectives.

However, although the gene at the CMD2 locus, which functions most effectively in SLCMV resistance, has been identified in recent years, there is a lack of discussion on the relationship between mutations on CMD2 locus and the level of SLCMV symptoms.

The author needs to discuss two peroxidases near the CMD2 locus in the discussion section. Do these two types of gene changes occur during SLCMV infection?

Also, are there any special SNPs in the genes near the CMD2 locus? I think a partial revision of the Discussion section is necessary.

Regarding the quantitative of SMARTsequencing,

The number of HiFi Reads in Table 2 varies greatly among samples. Please explain whether this data reflects the amount of transcription and what statistical processing was performed.

Please increase the resolution of the figures. The text in Figures 2b, 2c, and 2d, and Figs. 3a, 3b, and 3c are difficult to see.

Please show the information of original or raw data of SMART sequencing obtained from Gene Expression Omnibus etc.

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Reviewer #1: Yes:  Manas R. Sahoo

Reviewer #2: No

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<p>Comparative analysis of pattern-triggered and effector-triggered immunity gene expression in susceptible and tolerant cassava genotypes following begomovirus infection

PONE-D-24-29673R1

Dear Dr. Rey,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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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 #2: 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 #2: Yes

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

Reviewer #2: I Don't Know

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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 #2: 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 #2: Yes

**********

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 #2: Your responses to the comments are detailed, accurate, and well-writing, addressing the points raised comprehensively. I appreciate the clarity and effort you have put into them. Therefore, I will accept it.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files.

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

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy .

Reviewer #2: No

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