-->PONE-D-25-66187-->-->Both conventionally and organically fertilized tomatoes maintain fruit quality through uncontrolled green peach aphid infestation, with a transcriptional shift towards catabolism-->-->PLOS One

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Reviewer #1: This manuscript shows Tomatoes produced using both the conventional and organic fertilizer maintained similar yield and quality through uncontrolled green peach aphid infestation, by maintaining biochemical properties and transcriptional shift towards catabolic processes. This study is significant as it extensively assesses the interaction between aphid infestation and organic systems to provide insights on developing improved pest management strategies and identifying targets for crop improvement. The study is well designed and comprehensive as authors compared tomato plants grown in organic or conventional fertilizer with or without aphid infestation and used leaf and fruit tissues for biochemical and transcriptomic profiling. While the manuscript looks technically sound and the data provided supports the conclusion, I have following comments and suggestions to improve the manuscript:

1. Authors stated significantly lower nitrogen content resulting in the lower amino acid availability in the phloem maybe be the limiting factor for aphids in the plants grown in organic fertilizer and supported it with the literature (Mattson WJ 1980 Annu Rev Ecol Systm). I would suggest authors to add more reports to the discussion section on the role of nitrogen and amino acids in aphid infestation of plants.

2. In addition to nutrient and plant defense responses, I would recommend authors to discuss the role of soil microbiome in aphid-plant interactions in organic vs conventional farming practices and provide relevant references.

3. Authors tested the effect of aphid infestation on the yield of tomato plants in conventional vs organic fertilizer (Table 1). I would suggest author to add more information to the material and method sections Line 117 on growth stage of aphids added/counted, timepoint and method of counting.

4. Authors should add more information to the table and figure legends like number of plants (N) and type of statistical method used.

5. The quality of images is very poor in Figure 1 and Figure 2 of the manuscript PDF file and it’s hard to understand the axis labels. This may have been caused during file conversion, as the attached PNG images look good. I would suggest authors to check this and see if they can improve the image quality.

6. Line 232: I would suggest authors to edit the sentence to make it clear that Cluster dendogram for leaf and fruit are shown in Figure1 and Figure 2 respectively.

7. Line 234: Same as line 232, authors should make it clear that correlation plots in the gene co-expression network for leaf and fruit samples are shown in Figure 3 and Figure 4 respectively.

Reviewer #2: 1. The manuscript would benefit from clearer reporting of the statistical framework used for trait comparisons. Please specify the exact model structure (e.g., two-way ANOVA with fertilizer and aphid treatment as fixed effects), confirm whether interaction terms were tested throughout, and indicate how assumptions (normality, homoscedasticity) were evaluated. Where feasible, reporting exact p-values and degrees of freedom (possibly in supplementary material) would improve transparency.

2. Several figure captions, particularly for module–trait correlation heatmaps and GO enrichment analyses, lack sufficient detail to be interpreted independently. Please clarify color scales, significance thresholds, and whether GO enrichment results are corrected for multiple testing. Additionally, terminology such as “organic fertilizer treatment,” “organic production,” and “organic growing system” is used interchangeably throughout the manuscript; standardizing this language would improve clarity.

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Reviewer #1: No

Reviewer #2: Yes: RAMGOPAL PRAJAPATI

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Both conventionally and organically fertilized tomatoes maintain fruit quality through uncontrolled green peach aphid infestation, with a transcriptional shift towards catabolism

PONE-D-25-66187R1

Dear Dr. Dhingra,

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Kind regards,

Mohammad Irfan, Ph.D.

Academic Editor

PLOS One

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