All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
Both reviewers have agreed that their comments and concerns from the first revisions have been addressed and no further concerns were raised. Thank you to the reviewers and authors for your thorough reviews and edits, I recommend this manuscript for acceptance.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
The manuscript has been revised according to the reviewer's suggestion.
The manuscript has been revised according to the reviewer's suggestion.
The manuscript has been revised according to the reviewer's suggestion.
The manuscript has been revised according to the reviewer's suggestion.
In this resubmission, authors addressed my concerns in the first submission. I don't have further questions.
Authors added details about the "injury method" and qPCR quantification result table, which addressed my concerns in the first submission.
No comment
This is an interesting manuscript on the characterization of the AP2/ERF gene family in loblolly pine, a species with a large complex genome. Two reviewers agreed that minor revisions are needed but that the study is well-conducted and detailed.
I request that the authors consider each of the reviewers' comments and address these. In particular, more details are needed in the methods section on the treatment protocols applied. I agree with one of the reviewers that the gene expression quantification data should be provided in the supplementary information or made available publicly online for transparency.
**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.
1）The Latin name of Loblolly pine only needs to be marked in the title, abstract and text where it first appears.
2）Line 26-29“ the AP2/ERF gene family was identified in the whole loblolly pine genome using bioinformatics methods and by systematically analyzing its gene characteristics, physicochemical properties, phylogenetic evolution, promoter cis-elements, expression pattern, and potential functions. ” should be deleted. The sentence is repeated with the subsequent content of the abstract.
1)Line 194, the mechanical injury was not clearly discribed the specific method.
2)Line 189-Line 205, It was not clear how many seedlings were treated respectively, including 3 controls and 3 treatments.
There are no direct evidence shows that the conclusion of Line 558 "these members may be involved in the regulation of resin biosynthesis".
All of the Latin name of plants should be italics.
This article presents a detailed survey of AP2/ERF gene family in loblolly pine. Writing is clear, figures and tables are straightforward. However, I did not find the raw data of those ten gene expression quantifications. I think those data should be publicly shared.
Some methods require more description.
1. I feel more description is needed on treatment protocol. For instance, how did you perform “mechanical injury” treatment? Also, please simply explain the function of “Eth” and “MeJA”, I suppose they are provoking resin production. How did you implement such “treatment”? Did you inject or spread the chemical solution? Please clarify.
2. Line385-Line389, to prove the association between DRE/CRT/GCC and PtAP2/ERF TFs, a statistic test, such as hypergeometric test, is better than just showing numbers.
3. Line390-Line403, what statistical methods and threshold P-values were used for GO/KEGG Enrichment analyses? Details like these can help readers assess the importance of the identified terms.
4. Line415-Line433, statistical threshold is necessary to describe these gene expression profiles.
A “limitation and shortcomings” part should be added in "Discussion". As far as I know, scaffolds of loblolly pine have not been assembled to chromosomes. Does it affect the results of your gene family/gene element survey?
Typos such as Line79, “n”; Line82, typo “I” ......
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.