PONE-D-24-13936Transcriptomic analysis reveals effects of fertilization towards growth and quality of Fritillariae thunbergii  bulbusPLOS ONE

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Academic Editor

PLOS ONE

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Additional Editor Comments:

Two reviewers have provided valuable feedback. Please respond to their comments and make appropriate additions to the article.

Additional Comments from PLOS Editorial Office:

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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: Partly

Reviewer #2: Yes

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

Reviewer #1: I Don't Know

Reviewer #2: 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: Yes

Reviewer #2: 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: 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 Abstract is lacking key results like the yield and alkaloids content obtained from the best fertilizer.

In the introduction, is is preferable to state the hypothesis tested rather than the objectives.

In the methods section, the authors should justify why they use only one cultiver rather than using many. the quantity and justification of the quantity of eah of the fertiliser used for the study. what was the growing conditions of the plants. Alkaloids content was evaluated of plant tissue of how old? You should use AOVA test with mean separation as a statistical means. Also provide The software used for clustering transcriptome data

Reviewer #2: The manuscript entitled "Transcriptomic analysis reveals effects of fertilization towards growth and quality of Fritillariae thunbergii bulbus" provides valuable insights into optimizing the cultivation conditions of Fritillariae thunbergii (FTB), a traditional Chinese medicine renowned for its medicinal properties. The study investigates the impact of different fertilizers on the yield and quality of FTB, focusing on raw chicken manure (RC), organic fertilizer (OF), and plant ash (PA). Through a combination of HPLC-ELSD detection and yield statistics, OF application emerged as the most effective fertilizer. Transcriptome analysis uncovered the up-regulation of the ABA signaling pathway, potentially enhancing bulb yield, along with the identification of key genes associated with steroidal alkaloid accumulation. However, the manuscript requires minor revisions. Specifically, replication information regarding biological and technical replicates should be provided, and transcription factor/gene names should be italicized throughout the manuscript. Additionally, the methodology section should include NCBI SRA submission information. Furthermore, the introduction and discussion sections would benefit from the inclusion of references such as (Kumar, V., Sharma, S., Kumar, P. (2024). Insight into the Genetics and Genomics Studies of the Fritillaria Species. In: Gahlaut, V., Jaiswal, V. (eds) Genetics and Genomics of High-Altitude Crops. Springer, Singapore. https://doi.org/10.1007/978-981-99-9175-4_4; https://doi.org/10.1016/j.indcrop.2023.117541; Kumar, V., Kumar, P., Bhargava, B. et al. Transcriptomic and Metabolomic Reprogramming to Explore the High-Altitude Adaptation of Medicinal Plants: A Review. J Plant Growth Regul 42, 7315–7329 (2023). https://doi.org/10.1007/s00344-023-11018-8; Kapoor, B., Kumar, A. & Kumar, P. Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. Mol Genet Genomics 296, 1177–1202 (2021). https://doi.org/10.1007/s00438-021-01821-x) to enrich the context and support the findings. Overall, these adjustments will enhance the clarity and completeness of the manuscript, contributing to its scientific significance.

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Reviewer #1: Yes: Eric Bertrand Kouam

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-24-13936. review Kouam.pdf

Transcriptomic analysis reveals effects of fertilization towards growth and quality of Fritillariae thunbergii  bulbus

PONE-D-24-13936R1

Dear Dr. Fu,

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,

Minhui Li, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for your contributions to the field.

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: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: 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: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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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: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #3: 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: Susbtancial improvement has been carried out in the revised manuscript. I am satisfied with the answers provided to the different questions that was raised.

Reviewer #2: The authors have carefully addressed the comments and duly incorporated in the revised manuscript. Hence manuscript can be accepted in its current form.

Reviewer #3: The author has revised the paper as requested and responded to the questions. I agree to publish this manuscript in Plos one

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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 #1: Yes: Eric Bertrand Kouam

Reviewer #2: No

Reviewer #3: Yes: Jingmao You

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