Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas

Yuehui Tang; Wei Cheng; Shen Li; Ying Li; Xiang Wang; Jiatong Xie; Yingying He; Yaoyu Wang; Yiru Niu; Xinxin Bao; Qian Wu

doi:10.1371/journal.pone.0254711

Peer Review History

Original SubmissionMarch 23, 2021
21 Apr 2021 Decision Letter - Baohong Zhang, Editor PONE-D-21-09573 Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas PLOS ONE Dear Dr. Tang, 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 Jun 05 2021 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. 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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 ****** 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: 1.Figure 3: It is recommended that the authors rename motif 1 and 2 to WRC and QLQ to be more intuitive. 2.Figure 7B: It is recommended to indicate the treatment represented by each color. 3.154-155 line: You used two strategies instead of only blastP search. 4.Figure 4: Why is each chromosome labeled in a different color and with a different range? Is there any special meaning? 5.Figure 1: The author needs to be in the analysis of evolution bootstraps values marked in the Figure, high bootstraps values on the branch gene deserves more attention, at the same time can also be found JcGRF genetic relationship with the distance of GRF gene in different species. 6.The author needs to explicitly refer to the source of the software used, such as Line 110, MEGA 11 software. 7.91-92 line: It is suggested that the authors submit the protein sequences of candidate genes to the NCBI CDD (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and SMART (http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1) databases for the presence of the conserved domain of GRF. 8.It is recommended to add analysis experiments to make the article more complete, such as Gene Ontology annotation, Cis-acting elements analysis. 9.It is better to put a separate paragraph on the brief introduction of content of this study (lines 75-82) and it should briefly introduce the significance and value of this research. ****** 6. 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Revision 1
16 Jun 2021 Author Response Dear editor and reviewers: We thank you very much for giving us an opportunity to revise our manuscript. Furthermore, thank you for your comments and suggestions concerning our manuscript entitled “Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas”. The comments have all been very helpful to us in revising and improving our paper, as well as being of value in guiding our research. We have studied the comments carefully and have made corrections which we hope will meet with your approval. Revised portions of the paper are marked in red. In addition, the paper has been edited by a native-English speaker with a PhD in a relevant discipline working for the professional editing company Sees-editing Ltd. We hope you will consider this work for publication in PLos One. Thank you again for your consideration. Comments to the Author Reviewer #1: 1. Figure 3: It is recommended that the authors rename motif 1 and 2 to WRC and QLQ to be more intuitive. Response: Firstly, special thanks to you for giving me the opportunity to modify our paper. Secondly, thank you very much for your suggestion and your good comments. We have rename motif 1 and 2 to WRC and QLQ in the revised MS. 2. Figure 7B: It is recommended to indicate the treatment represented by each color. Response: Special thanks to you for your good comments. We have added the treatment represented by different color in the revised MS, in the Figure 7B. 3. 154-155 line: You used two strategies instead of only blastP search. Response: We appreciate for Reviewers’ suggestion. This is an important point that we should have mentioned. According to your advice, we have added two strategies instead of only blastP search in lines 160-161, the revised MS. 4. Figure 4: Why is each chromosome labeled in a different color and with a different range? Is there any special meaning? Response: We appreciate for Reviewers’ comments. We use a different length color mainly for the purpose of making it easier for readers to find the location of the JcGRF proteins on the chromosome, and on the other hand for aesthetics. 5. Figure 1: The author needs to be in the analysis of evolution bootstraps values marked in the Figure, high bootstraps values on the branch gene deserves more attention, at the same time can also be found JcGRF genetic relationship with the distance of GRF gene in different species. Response: Special thanks to you for your good comments. According to your advice, we have added the bootstraps values on the branch in the phylogenetic tree in Figure 1, as shown in the Revised MS. 6. The author needs to explicitly refer to the source of the software used, such as Line 110, MEGA 11 software. Response: We appreciate for Reviewers’ suggestion. We have added references about MEGA X. We hope you will consider this work for publication in PLos One. Thank you again for your consideration. 7. 91-92 line: It is suggested that the authors submit the protein sequences of candidate genes to the NCBI CDD (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and SMART (http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1) databases for the presence of the conserved domain of GRF. Response: We appreciate for Reviewers’ suggestion. Thank you for your suggestion. All GRF family candidate genes of Jatropha curcas have been uploaded to the NCBI database, and the gene numbers are shown in Table 1, in the revised MS. 8. It is recommended to add analysis experiments to make the article more complete, such as Gene Ontology annotation, Cis-acting elements analysis. Response: Thank you very much for your good suggestion. According to your advice, we have added data on the analysis of cis-acting elements of the GRF gene, in lines 119-123, and 240-256, in the revised MS, as shown in S3 File. 9. It is better to put a separate paragraph on the brief introduction of content of this study (lines 75-82) and it should briefly introduce the significance and value of this research. Response: We appreciate for Reviewers’ comments. We have made the modification according to your request. We hope you will consider this work for publication in PLos One. Thank you again for your consideration. Attachments Attachment Submitted filename: Respone to editor and Reviewers.docx https://doi.org/10.1371/journal.pone.0254711.r002
2 Jul 2021 Decision Letter - Baohong Zhang, Editor Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas PONE-D-21-09573R1 Dear Dr. Tang, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Baohong Zhang, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0254711.r003
Formally Accepted
8 Jul 2021 Acceptance Letter - Baohong Zhang, Editor PONE-D-21-09573R1 Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas Dear Dr. Tang: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Professor Baohong Zhang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0254711.r004

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