PONE-D-22-15697Transcriptome analysis of female western flower thrips, Frankliniella occidentalis, exhibiting neo-panoistic ovarian developmentPLOS ONE

Dear Dr. Kim,

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Reviewers' comments:

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

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Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: Reviewer’s comment

Title: Transcriptome analysis of female western flower thrips, Frankliniella occidentalis, exhibiting neo-panoistic ovarian development.

In this study, the authors Choi and Kim have done transcriptome analysis of pest western flower thrips Frankliniella occidentalis at mid (36 h after adult emergence (AAE)) and late (60 h AAE) ovarian developmental stages using RNA sequencing (RNASeq) technology. More than 120 million reads per replication were matched to » 15,000 F. occidentalis genes. Almost 500 genes were expressed at each mid and late ovarian developmental stage. Differentially expressed genes (DEGs) were associated with metabolic pathways and protein and nucleic acid biosynthesis. In both ovarian developmental stages, vitellogenin, mucin, and chorion genes were highly (> 8-fold) expressed. Endocrine signals associated with ovarian development were further investigated from the DEGs. Insulin and juvenile hormone signals were upregulated only at 36 h AAE, whereas the ecdysteroid signal was highly maintained at 60 h AAE.

The thrip is the primary vector for a few plant viruses such as tomato spotted wilt virus (TSWV) and impatiens necrotic spot virus (INSV). The study is interesting and vital as the thrips can destroy many crops worldwide by feeding on them and by spreading the plant viruses. There are few reports on the transcriptomic analysis of the thrips during virus infection, but that of on reproduction of F. occidentalis is rare in the literature. However, the discussion part is important here. The RNA/gene expression results are straight forward but how these differentially expressed genes contribute to a faster reproduction rate needs to be discussed in detail. Here are few suggestions which might improve the value of the manuscript.

1. Discussion: How these results help in the control of the pest directly or indirectly needs to be explained. What is the significance of expressed genes? The authors may consider including literature support on this aspect.

2. Resolution of figures 3, 4 and 5 to be improved.

3. Line 98-99: Mention that the total RNA extracted was from the whole thrips.

4. As this article is on the reproduction of thrips and hence, more detail related to reproduction can be included in the introduction. How fast the pest can develop into an adult (Moritz et al. 2004. Virus Res., 100 pp. 143-149), etc.

5. The transcriptomics results need not necessarily correlate to protein expression (PMID: 26085669). Authors may consider including it in the discussion.

Reviewer #2: The article by Choi et al. summarizes ovarian development and associated transcriptomes of F. occidentalis at various stages of oocyte development (0 h AAE, 36 h AAE, and late 60 h AAE) and compares the differentially expressed genes. The study is technically well performed and described in the manuscript, yet there are some concerns that should be addressed before it can be reconsidered for publication.

1. Why do authors choose to perform RNA extraction from whole female adult F. occidentalis instead of just from the ovarioles?

2. In Figure 1, the authors have only shown one stage (3-day-old female adults) of ovariole structure. Since the authors are focusing on all three stages ( 0h, 36 h, and 60 h AAE) and are also measuring the ovariole length, it is important to show all stages of ovariole development.

3. For Figure 2B, it might be better to include volcano plots with differentially expressed genes pattern (36 vs 0, 60 vs 0, 36 vs 60) and top candidate gene names to guide readers to follow the changes in gene expression.

4. In Figure 3, it is difficult to follow the entire stretch of the graph. Importantly, the labels are not clearly legible. Authors can show only the pathways that are up or down-regulated between 60 vs 36 instead of showing the number of genes.

5. Figures 4 & 5: Authors may consider merging these two figures into one figure. Also, is there a particular reason for including RPKM values on the main figure?

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Reviewer #1: No

Reviewer #2: Yes: Prasanna Katti

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Submitted filename: Reviewers comment-PONE-D-22-15697.docx

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Submitted filename: Choi et al., 2022_.docx

Transcriptome analysis of female western flower thrips, Frankliniella occidentalis, exhibiting neo-panoistic ovarian development

PONE-D-22-15697R1

Dear Dr. Kim,

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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Academic Editor

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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 #1: (No Response)

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 #1: Partly

Reviewer #2: Yes

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

Reviewer #1: I Don't Know

Reviewer #2: N/A

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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 #1: No

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 #1: Yes

Reviewer #2: 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 #1: The author's responses are satisfactory. However I could not locate the revised figures. Not sure if there is any technical error?

Reviewer #2: (No Response)

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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.

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Reviewer #1: No

Reviewer #2: No

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