Genome-wide identification of the bZIP transcription factor family and expression analysis under abiotic stress in Zanthoxylum bungeanum

Changming Liu; Zhiguo Tian; Feng Xian

doi:10.1371/journal.pone.0324447

Peer Review History

Original SubmissionMarch 17, 2025
17 Mar 2025 Author Response https://doi.org/10.1371/journal.pone.0324447.r001
8 Apr 2025 Decision Letter - Shailender Kumar Verma, Editor PONE-D-25-14248Genome-Wide Identification of bZIP Transcription Factors Family and Analysis of Its Expression Under Abiotic Stress in Zanthoxylum BungeanumPLOS ONE Dear Dr. Liu, 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. Please submit your revised manuscript by May 23 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Shailender Kumar Verma, Ph.D. Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating the following financial disclosure: [This research was funded by Agricultural Innovation and Driven Project of Shaanxi Province, China (No. Shaanxi Agricultural Planning and Finance [2022]29); Shangluo University Industrialization Incubation Project (No. 21CK04)]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. 4. Please amend your authorship list in your manuscript file to include author Feng Xian ,. Additional Editor Comments (if provided): [Note: HTML markup is below. Please do not edit.] 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: Yes Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ****** 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 ****** 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 ****** 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: This manuscript focused on bioinofrmatic analyses of bZIP transcription factors in zanthoxylum bungeanum, and provided a comprehensive acquaintance of molecular mechanism of bZIP genes in response to multiple abiotic stresses. Generally, we believe this manuscript are of innovation and significance for bZIP studies, while many technical issues must be put forward first. (1)The writing of the manuscript needs improvement, and suggest to invite one professional researcher to polish this article. (2)Line 163, revise 21 as twenty-one, since the sentences should start with capital letters. (3)We noticed that the authors performed qRT-PCR experiments on the chosen bZIP genes for expression-pattern investigation, however, the consistency between qRT-PCR and RNA-seq was low. Suggest to re-chose some ones to conduct qRT-PCR experiment, or draw the correlation coefficient figure. (4)Why not to perform VIGS experiment to verify the potential genes ? Reviewer #2: The manuscript mainly identifies the bZIP gene family, but due to the large number of members, the authors did not do some common bioinformatics analyses such as gene structure, physicochemical properties and chromosomal localisation, but the current authors' collation of some databases also provides data support for the identification of the bZIP gene family of Zanthoxylum Bungeanum. The details are as follows: 1. The author was advised to change the title; for example: “Genome-wide identification of the bZIP transcription factor family and expression analysis under abiotic stress in Zanthoxylum Bungeanum.” 2. Lines 19-20: Please replace ‘higher activity’ with ‘high expression’ or ‘higher transcript abundance’. Please check the full text for similar issues. 3. Please add ‘bioinformatics analyses’ to keywords section. 4. The authors were advised to change the order of the introduction section. The authors were asked to first describe the abiotic stresses encountered in growing peppers (third paragraph of the introduction), then go on to describe the plant damage of the abiotic stresses (first paragraph of the introduction), then describe the role of bZIP in the abiotic stresses (second paragraph of the introduction), and finally lead in with what was done in the study? What was the significance of doing the study? Please ask the authors to be aware of the connection and logic between each paragraph in their descriptions. 5. The methods of data analysis are missing from the Materials and Methods section. Authors are requested to check for formatting problems in the subheadings. 6. It is recommended that the authors explain in the materials and methods why 250 mmol/L NaCl solution was chosen and why different time points were chosen to collect the samples. 7. It is suggested that the author modify the representation of the figure notes in the result part, some of which are abbreviated, and some are full names. It is suggested that the author carefully modify according to the format requirements of the journal 8. The authors were advised to re-describe the results section; the current description is too heavily colloquial and unlike the form of writing a scientific paper. For example: Lines 245-248. The authors can specifically describe how many-fold the expression of bZIP genes is repressed under abiotic stress and how they trend. Please ask the author to check the tenses throughout the text. ****** 6. 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: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0324447.r002
Revision 1
21 Apr 2025 Author Response Manuscript ID: PONE-D-25-14248 MS TITLE: Genome-Wide Identification of bZIP Transcription Factors Family and Analysis of Its Expression Under Abiotic Stress in Zanthoxylum Bungeanum Dear editor and reviewers, We sincerely appreciate the critical comments and thoughtful suggestions provided by you and the reviewers, as they have greatly contributed to revising and improving our paper, as well as guiding our future research endeavors. We have thoroughly examined the comments and made necessary corrections in accordance with your feedback. Please refer to my itemized responses below and find the revised/corrected versions in the re-submitted files. Editor: Question 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. Answer: According to your suggestion, we have made corrections according to the style requirements of the journal, adjusted the font size of the title, and removed the number prefix of the title, for example: 1. Introduction was changed to Introduction. And the title is capitalized with the first letter of the word. Change the icon format in the support information, for example Fig S1 to S1 Fig. If there is any need for more modification, we will further improve it according to the subsequent suggestions. Question 2. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Answer: The two funders are the source of funding for the study. They are not specifically involved in research design, data collection and analysis, publication decisions, or manuscript preparation. We have disclosed the funding statement in our cover letter and manuscript. Please check these contents. Question 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. Answer: Thank you for reminding us that we have associated the ORCID ID before submitting the revised manuscript. Question 4. Please amend your authorship list in your manuscript file to include author Feng Xian. Answer: We are sorry that due to an oversight and mistake, one of authors was not mentioned in the manuscript. We have included the author in the manuscript (Line 3 in revised manuscript). Reviewer #1: This manuscript focused on bioinofrmatic analyses of bZIP transcription factors in zanthoxylum bungeanum, and provided a comprehensive acquaintance of molecular mechanism of bZIP genes in response to multiple abiotic stresses. Generally, we believe this manuscript are of innovation and significance for bZIP studies, while many technical issues must be put forward first. Question 1. The writing of the manuscript needs improvement, and suggest to invite one professional researcher to polish this article. Answer: Thank you for your thoughtful advice. We have engaged two professional researchers to optimize the writing of our manuscript. Proof of retouching from this institution is on the last page of this document. Question 2. Line 163, revise 21 as twenty-one, since the sentences should start with capital letters. Answer: Your suggestion is reasonable. We have modified 21 to twenty-one (Line 177 in revised manuscript). Question 3. We noticed that the authors performed qRT-PCR experiments on the chosen bZIP genes for expression-pattern investigation, however, the consistency between qRT-PCR and RNA-seq was low. Suggest to re-chose some ones to conduct qRT-PCR experiment, or draw the correlation coefficient figure. Answer: Thank you for the suggestion. Our core genes showed differences in expression trends between qRT-PCR and RNA-seq. Although we used the same cultivars, breeding methods, and stress treatments, there may be differences in genetic background from those used for RNA-seq. In particular, the transcriptomes involved are from three different experiments. This difference in genetic background may have contributed to this error. Secondly, there are also differences between the two technical measures, which will affect the consistency of their expression trends. However, it is worth affirming that the overall trend of our qRT-PCR is consistent with that of RNA-seq. Question 4. Why not to perform VIGS experiment to verify the potential genes? Answer: Thank you for your constructive suggestions. In fact, Zanthoxylum Bungeanum is an allotetraploid plant, and there is a lack of mature technology for VIGS experiments. At present, we lack the experience of gene verification work, and we will gradually try to verify its possibilities on model plants in the future. Reviewer #2: The manuscript mainly identifies the bZIP gene family, but due to the large number of members, the authors did not do some common bioinformatics analyses such as gene structure, physicochemical properties and chromosomal localisation, but the current authors' collation of some databases also provides data support for the identification of the bZIP gene family of Zanthoxylum Bungeanum. Question 1. The author was advised to change the title; for example: “Genome-wide identification of the bZIP transcription factor family and expression analysis under abiotic stress in Zanthoxylum Bungeanum. Answer: Thank you for your valuable advice. We have changed the title to "Genome-wide identification of the bZIP transcription factor family and expression analysis under abiotic stress. in Zanthoxylum Bungeanum". (Lines 1-2 in revised manuscript) Question 2. Lines 19-20: Please replace ‘higher activity’ with ‘high expression’ or ‘higher transcript abundance’. Please check the full text for similar issues. Answer: According to your suggestion and the polishing suggestions of professional researchers, we will modify the corresponding content. We hope our modification conforms to your ideas, please refer to Lines 19-20 for details. Question 3. Please add ‘bioinformatics analyses’ to keywords section. Answer: Thank you for your thoughtful advice. We have added bioinformatics analysis to the keyword section (Line 25 in revised manuscript). Question 4. The authors were advised to change the order of the introduction section. The authors were asked to first describe the abiotic stresses encountered in growing peppers (third paragraph of the introduction), then go on to describe the plant damage of the abiotic stresses (first paragraph of the introduction), then describe the role of bZIP in the abiotic stresses (second paragraph of the introduction), and finally lead in with what was done in the study? What was the significance of doing the study? Please ask the authors to be aware of the connection and logic between each paragraph in their descriptions. Answer: Thank you for giving us these good suggestions. As requested, we have adjusted the order of the paragraphs in introduction section. In addition, the reference numbers have also been adjusted accordingly (Lines 27-53 in revised manuscript). We hope that the revised paragraph structure will meet with your approval. Question 5. The methods of data analysis are missing from the Materials and Methods section. Authors are requested to check for formatting problems in the subheadings. Answer: According to your suggestion, here we refer to other relevant studies [1-2], optimize this part, and supplement the relevant content (Lines 70-71, 92-95, 104-105, and 122-123 in revised manuscript). We hope that the corresponding changes to your question can be approved by you and if this part needs further improvement, we would like you to point out the specific problems. Thank you very much. [1] Wang S, Hu W, Zhang X, Liu Y, Liu F. Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members in Zanthoxylum bungeanum and Their Expression Profiles in Response to Abiotic Stresses. Plants [Internet]. 2025; 14(4). [2] Du H, Feng BR, Yang SS, Huang YB, Tang YX. The R2R3-MYB Transcription Factor Gene Family in Maize. Plos One. 2012;7(6). doi: 10.1371/journal.pone.0037463. PubMed PMID: WOS:000305351700006. Question 6. It is recommended that the authors explain in the materials and methods why 250 mmol/L NaCl solution was chosen and why different time points were chosen to collect the samples. Answer: Thank you for the suggestion, and we cited the sources of three stress treatment methods in the section of “Plant materials and expression pattern analysis of ZbbZIPs” (Lines 104-105 in revised manuscript: The cultivation and stress treatment of the plant materials were based on the methods of Tian (cold stress), Hu (drought stress) and Nie (salt stress) [2,5,24]). Question 7. It is suggested that the author modify the representation of the figure notes in the result part, some of which are abbreviated, and some are full names. It is suggested that the author carefully modify according to the format requirements of the journal Answer: Thank you for your thoughtful suggestion. We modified the figure notes in the result part and unified them into "Fig" according to the requirements of the journal (Lines 222, 225 and 274 in revised manuscript). Question 8. The authors were advised to re-describe the results section; the current description is too heavily colloquial and unlike the form of writing a scientific paper. For example: Lines 245-248. The authors can specifically describe how many-fold the expression of bZIP genes is repressed under abiotic stress and how they trend. Please ask the author to check the tenses throughout the text. Answer: According to your suggestion, we have redescribed the results section, and at the same time invited two professional researchers to optimize the writing of our manuscript. Proof of retouching from this institution is on the last page of this document. In particular, the sections you mentioned (Lines 245-248) are scientifically detailed (Lines 264-272 in revised manuscript). We hope that the revision of this manuscript can receive your approval. Once again, thank you very much for your kind comments and suggestions. We look forward to your information about our revised paper. Best wishes for you! Yours sincerely, Changmin Liu Attachments Attachment Submitted filename: Response Letter.docx https://doi.org/10.1371/journal.pone.0324447.r003
25 Apr 2025 Decision Letter - Shailender Kumar Verma, Editor Genome-wide identification of the bZIP transcription factor family and expression analysis under abiotic stress in Zanthoxylum bungeanum PONE-D-25-14248R1 Dear Dr. Liu, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Shailender Kumar Verma, Ph.D. Academic Editor PLOS ONE 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: All comments have been addressed Reviewer #2: All comments have been addressed ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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 ****** 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 ****** 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: This manuscript focused on bioinofrmatic analyses of bZIP transcription factors in zanthoxylum bungeanum, and provided a comprehensive acquaintance of molecular mechanism of bZIP genes in response to multiple abiotic stresses. Generally, we believe this manuscript are of innovation and significance for bZIP studies, and all the incorrect portions have been modified in this manuscript. The revised article has met the standard for publication. Reviewer #2: (No Response) ****** 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: No Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0324447.r004
Formally Accepted
Acceptance Letter - Shailender Kumar Verma, Editor PONE-D-25-14248R1 PLOS ONE Dear Dr. Liu, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Shailender Kumar Verma Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0324447.r005

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .