PONE-D-23-08909Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in TrichodermaPLOS ONE

Dear Dr. Scott,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

This was an interesting study that is likely to have far-reaching implications for understanding fungal endophytes going forward. I apologize for the delay in getting this back to you, I lost contact with one reviewer. However, I have read the manuscript thoroughly and I agree with Reviewer 1's assessment of the work. Please attempt to address all their comments as throughly as possible.

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"This work was supported by a grant from the National Science Foundation (DEB-1638999) to JCS and by a Marie Skłodowska-Curie Individual Fellowship (SEP-210615880-TRADEOFF) to EGT."

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Reviewer #1: Yes

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

Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: The manuscript by Scott et al is a comprehensive comparative genomic analysis of Trichoderma genomes. I have a few suggestions for improvement.

1. Please define the terms mycotrophy and saprotrophy. For mycotrophy in particular, it was unclear to me how this term relates to endotrophy and mycoparasitism.

2. I'd encourage the authors to read through the results section again carefully and add additional references throughout. Example statements that are missing attribution include lines 217, 221, 244, 884. References for Bloomberg's K, Pagel's Lambda, Fritz and Purvis' D-statistic are provided in the methods, but i think it would be helpful to include their references in the results section as well (lines 280, 293).

3. Can the author's perform a topology test to confirm that a constrained phylogeny in which Trichoderma easA genes group with other Hypocreales is significantly worse than the unconstrained best tree? I think this would be a nice additional bit of evidence to support the claim of HGT.

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Reviewer #1: No

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Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

PONE-D-23-08909R1

Dear Dr. Scott,

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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Kind regards,

Richard A Wilson

Academic Editor

PLOS ONE

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