Comparative Transcriptomic Analysis Reveals Variable Responses to the Brown Planthopper Nilaparvata lugens in Different Rice Cultivars

Round 1

Reviewer 1 Report

Lot of work in this direction has been published were BPH was used in different varieties and RNA seq was made in various tissues. Moreover, no information reported on level of infestation, metabolomics status of genotypes, performance of genotypes during BPH infestation, etc. 

On which report these three lines were selected provide reference

 L77: at which stage of plant, BPH were released.  How BPH were reared in lab. Is this a special BPH culture managed in lab

L131: Which make/model of RTPCR was used

Overall there is lack of novelty in article

Discussion is very much weaker and less related with results. 

Sorry, i can not recommend this article for publication especially in current form.

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

I have specific suggestions to improve the manuscript:

Introduction: Need comprehensive review on transcriptome analysis of Bph infection in rice.

L 60-65, L 70 and Fig 1: These paragraphs can be revised for clarity and removed to Materials and Methods (M&M). 

L71: Plant materials must be described in more detail in terms of resistance to Bph. It can be removed to M&M under a new Plant Materials. Also authors must describe biotypes of the Bph used in your experiment.

L135: Can be removed to M&M to describe your quality data. Table 1 can be set as a Supplement Table.

L137: Data quality standard referred to Table 1 needed a reference and removed to M&M.

Fig 2: Can be removed to M&M to describe the data quality.

L155-157: Please revise the sentence "In HR05...."

L158-168: The data can be presented as Supplement Tables.

Fig 4: More describe Patterns a-f.

L178: What are "terms" refer to.

L183: Please fix the quality of Fig 5b and 5d.

 L199: Correct BPH not PBH

Fig 6 is hard to differentiate dots' colour clearly.

Fig 9 did not show a good correlation between qPCR and RNA seq results.

L268: Please correct "Pest controling"

 

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

Authors submitted manuscript entitled “Comparative transcriptomics analysis reveals variable responses to the brown planthopper, Nilaparvata lugens in different rice cultivars” to Crops journal. In this manuscript, authors have performed RNA-seq analysis to study the response of different rice genotypes in response to BPH feeding. Authors have generated enough data but failed to present in a comprehensive way. The presentation of hub or key genes in results section is missing. The discussion section is very short and not provides the key message of the obtained results. The main idea of the study is good but the manuscript needs substantial revisions before consideration. In addition, the references in discussion section are not inserted according to journal’s guidelines. I have following comments;

L31-32; revise this sentence.

Provide the detail of figure 1 in its legend.

Introduction section is very poor and does not provide the enough background and review of the study.

L113-114; Authors should use full form of different terms when they appears first and use abbreviations in subsequent sections.

Provide little detail about real time PCR in 2.5. section.

Authors should provide the accession numbers of the sequencing files if authors have submitted to any repository.

Provide the enough information regarding the used genotypes in this study.

L152; differentially expressed genes… DEGs… try to abbreviate when it comes first and then use abbreviations.

L159-165; Lipid metabolism, Glycan biosynthesis etc. no need to start these terms with capital letter.

L210; Gene names should be italicized.

3.5. and Figure 9; Authors selected 10 or 2 genes for RT-PCR? Please confirm it and revise accordingly.

Result section is very poor and findings are not presented in detail. Authors have focused on GO and KEGG but the key genes regulated in response to BPH feeding are not mentioned.

Discussion section is very weak and brief. Try to discuss the results in relevance to previously published literature and speculate the results as per the findings. In addition, provide the research gap statements and possible future directions. Moreover, citations are not according to the journal.

Authors should carefully check the grammar and other sentence mistakes.

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Author has revised the article, article may be accepted 

Author Response

Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions.

Reviewer 2 Report

Thank you for revising the manuscript as suggested

Author Response

Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions.

Reviewer 3 Report

Authors have addressed most of the comments. The format of the manuscript is not according to the journal guidelines, so it should be revised. 

Author Response

Thanks very much for taking your time to review this manuscript. I really appreciate all your comments and suggestions. We have revised the full manuscript, and relevant background and discussion are added. Please see the revised manuscript for details.