Comparative transcriptome analysis reveals key genes potentially related to organic acid and sugar accumulation in loquat

Jun Yang; Jing Zhang; Xian-Qian Niu; Xue-Lian Zheng; Xu Chen; Guo-Hua Zheng; Jin-Cheng Wu

doi:10.1371/journal.pone.0238873

Peer Review History

Original SubmissionMarch 4, 2020
17 Jun 2020 Decision Letter - Xiaoming Pang, Editor PONE-D-20-06341 Comparative Transcriptome Analysis Reveals Key Genes Potentially Related to Organic Acid and Sugar Accumulation in Loquat PLOS ONE Dear Dr. Zheng, 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 Aug 01 2020 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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Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 6. Please amend the manuscript submission data (via Edit Submission) to include author Jun Yang, Xue-Lian Zheng, Xu Chen. 7. Please amend your list of authors on the manuscript to ensure that each author is linked to an affiliation. Authors’ affiliations should reflect the institution where the work was done (if authors moved subsequently, you can also list the new affiliation stating “current affiliation:….” as necessary). 8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 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 ****** 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 ****** 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: The manuscript is well presented, and it is systematic analyses of major organic acids, sugar content, enzyme activities, and the expression of related genes during fruit development in two different loquat cultivars. It is well studied that the sugar content increased during fruit development, the organic acid content dramatically decreased in the later stages of fruit development. The DEGs in the later stages of fruit development between the two cultivars were analyzed in depth. The findings will help understand the molecular mechanism of organic acid and sugar formation in loquat, which will aid in breeding high-quality loquat cultivars. Some comments: -In the abstract part, the author only described the results and lacks summative sentences. -There is a lack of detailed description of the experimental materials, why these two experimental materials were used, why these three sampling times were chosen? -The genetic background of the two cultivars was somewhat different, so the credibility of DEGs was somewhat low. -There are only three sampling time points, and if there were more time points, the results would be more reliable. ****** 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 [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.0238873.r001
Revision 1
30 Jul 2020 Author Response Professor Xiaoming Pang Editor, Plos one July 8, 2020 Dear Dr. Xiaoming Pang Thank you so much for critiquing our submission titled "Comparative transcriptome analysis reveals key genes potentially related to organic acid and sugar accumulation in loquat." We reviewed the concerns from the reviewers and have improved our manuscript. We have also utilized the service of an English language editing company to improve the language and presentation of our manuscript. Therefore, we have incorporated the suggested changes and would like to resubmit our manuscript. We have incorporated the changes suggested by the reviewers and have answered their questions to the best of our ability. Please see our point-to-point responses below. Reviewer 1: 1. In the abstract part, the author only described the results and lacks summative sentences. We have added the summative sentence of the article from 2- Page 2, line 35–43 in the abstract part. 2. There is a lack of detailed description of the experimental materials, why these two experimental materials were used, why these three sampling times were chosen? We selected the cultivars ‘JiFangZhong’ and ‘BaiLi’ because ‘JFZ’ has high acid and low sugar, while ‘BL’ has low acid and high sugar. Both cultivars are late maturing, and have similar flowering patterns. In addition, we also provide pictures of the three periods of two varieties in S1 Fig. Therefore, the differences in sugar/acid ratios in the two cultivars would provide a good overview of their accumulation and metabolism and the related genes. Chen et al, Hirai M and Yang (reference 6, 9 and 12 in the revised manuscript) have showed that these three time points are the critical period during the accumulation of louquat fruit sugar and acid. Thus we chose these three developmental stages in this study. 3. The genetic background of the two cultivars was somewhat different, so the credibility of DEGs was somewhat low. A previous study by Chen et al. (reference 8 in the revised manuscript) have indicated that the two cultivars in this study all belong to Eriobotrya japonica Lindl. Thus, We think the two cultivars have a consistent genetic background.We have added Eriobotrya japonica Lindl to the title of the article. 4. There are only three sampling time points, and if there were more time points, the results would be more reliable. First, according to a large number of article (reference 6, 9 and 12 in the revised manuscript), the three periods selected in this paper are the three key periods for the accumulation of sugar and acid in loquat fruit. Then, Jiang et (in Supplementary literature) have showed that the flesh of pummelo cv. GXMY and its mutants HRMY and HJMY in three development periods of fruit were selected to investigate the candidate genes of carotenoid metabolism by the RNA-Seq technique. Besides, Zhang et (in Supplementary literature) have also showed that seeds of P. rockii and P. lutea at 20, 60 and 80 days were collected to study FA biosynthesis metabolism by the RNA-Seq technique. . Thus We think the three points taken in this article can explain the accumulation of sugar and acid mechanism during the development of loquat fruit. Format modification: We have modified the format strictly in accordance with the format requirements of Plos one. Editor's Comments to Author: Pay attention to the typos, for example, P43，polant families Organic acids related taste was repeated several times in such a short introduction.The rationale of present study and the use of the two cultivars was not well presented. We have modified the polant typo to plant, and have carefully checked other typos in the article. We have deleted some sentences about Organic acids related taste in introduction, such as P55 and P63. We have added some content about the rationale of present study and the use of the two cultivars in S1 Fig, P13, P68-72 and P84-87.if there are any further corrections necessary, we will be happy to incorporate them. We look forward to your response. Thanks again for helping us improve this submission for your esteemed journal. Best regards, Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0238873.r002
26 Aug 2020 Decision Letter - Xiaoming Pang, Editor Comparative Transcriptome Analysis Reveals Key Genes Potentially Related to Organic Acid and Sugar Accumulation in Loquat PONE-D-20-06341R1 Dear Dr. Zheng, 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, Xiaoming Pang, PhD 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: (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 https://doi.org/10.1371/journal.pone.0238873.r003
Formally Accepted
12 Apr 2021 Acceptance Letter - Xiaoming Pang, Editor PONE-D-20-06341R1 Comparative Transcriptome Analysis Reveals Key Genes Potentially Related to Organic Acid and Sugar Accumulation in Loquat Dear Dr. Zheng: 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 Dr. Xiaoming Pang Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0238873.r004

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