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Dear authors,
Happy to inform you that the manuscript, Comparative genome analysis of patulin-producing Penicillium paneum OM1 isolated from pears has been accepted for publication in the PeerJ journal.
Thanking you,
Sushanta Deb
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
Dear Dr. Om,
The manuscript you kindly submitted to PeerJ has been reviewed by experts in the field. Based on their evaluations, the reviewers have recommended minor revisions.
Reviewer comments are provided at the end of this letter. Please respond to each comment with a detailed, point-by-point reply.
Regards,
Sushanta Deb
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
The authors gave two different sections as Results and Discussion, but the results section includes some interpretive comments supported by references. These are technically the discussion part given in the Results section. It does blur the typical division between results reporting and discussion. This results in some redundancy and a long manuscript. Hence, it is suggested to rewrite the result section by trimming interpretive language and enriching the discussion section.
The protocols and software used for genome sequencing and analysis are well chosen.
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The manuscript is mostly well written, and the English language is good. Several sentences need some changes to enhance the text flow and clarity, and minor changes are needed regarding the use of articles (a, the) and writing numbers. I provided the suggestions in the PDF document derived from a Word document with the Track Changes option on.
The background of the research problem is well explained, and the literature used is relevant and quoted well.
Figures. Figures are relevant, clear, and understandable, well labelled and described. Almost all of them are of high quality, except for Figure 1, where there is some blur in it (not enough sharpness of the pie chart's legend). I hope and suppose that is because of the compression of the file while saving it as a PDF.
Fig 4A – I would suggest adding clarification about the percentage in the figure caption – „percentage below species and strain name represents genome similarity with P. paneum OM1“.
Raw data supplied – The authors provided a FASTA file (sequence assembly). As the reviewer, I was unable to verify that the assemblies or the read data are going to be publicly available. However, there is a note indicating that the data is being submitted to Genbank, and I would advise the editor to check with the other reviewer to inspect the data availability before approving the manuscript publication.
There are no remarks about experimental design; all of the PeerJ Editorial Criteria are met – original research with a well-defined main goal, state-of-the-art methods in this scientific field, and with enough details for study replication.
The authors presented new results and data about the biosynthetic gene clusters (BGCs) of patulin in the genome of Penicillium paneum (strain OM1). The impact and the novelty of the research are well and clearly stated, and the underlying data are robust and controlled. The discussion of the results is good, with relevant literature sources and a comprehensive comparison of their results with other studies. I want to give praise to the authors for commenting, both confirming and opposing studies, and for providing a possible explanation for the discrepancies between their results and the results of other researchers.
Part of the results were discussed and commented on with the literature sources in the Results section. I did not find that troubling (it was actually helpful to me), but the authors should consult the Handling Editor can those sentences: 1) stay there; 2) should be moved to the Discussion section; 3) or the sections of Results and Discussion can be joined (if the journal allows it), without the necessity to make bigger text rearrangment.
Conclusions are clearly presented, connected with the original research question, and limited to the obtained results.
It is OK
It is OK
It is OK
This study provides genome sequencing data and bioinformatic analysis of patulin-producing Penicillium paneum OM1, representing a meaningful contribution to the field. The following revisions would enhance manuscript clarity:
1. Relocate the genome assembly statistics to Figure 1, the orginal Figure 1 should be changed to Figure 2, which is beneficial to establish a logical analytical narrative.
2. use apple and pear instead of apples and pears.
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