Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L.

Janardan Khadka; Buzi Raviv; Bupur Swetha; Rohith Grandhi; Jeevan R. Singiri; Nurit Novoplansky; Yitzchak Gutterman; Ivan Galis; Zhenying Huang; Gideon Grafi

doi:10.1371/journal.pone.0237045

Peer Review History

Original SubmissionMay 5, 2020
24 Jun 2020 Decision Letter - Suprasanna Penna, Editor PONE-D-20-13034 Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L. PLOS ONE Dear Dr. Grafi, 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. The work presented in this manuscript has interesting results. Reviewers have pointed out that in the present form, it lacks methodological details, rationale for not having an important treatment, and details about statistical tools. Authors can re-work on the suggestions to improve overall presentation of their manuscript. Please submit your revised manuscript by Aug 08 2020 11:59PM. 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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. In your Methods section, please provide additional information regarding the permits you obtained for the seed collection. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. 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We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. In your revised cover letter, please address the following prompts: a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent. b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. We will update your Data Availability statement on your behalf to reflect the information you provide. Additional Editor Comments: The work presented in this manuscript has interesting results. Reviewers have pointed out that in the present form, it lacks methodological details, rationale for not having an important treatment, and details about statistical tools. Authors can re-work on the suggestions to improve overall presentation of their manuscript. [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: No Reviewer #2: I Don't Know ****** 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: In the proposed manuscript, the authors around G. Grafi have pursued their longstanding research topic to understand the role of dead maternal seed tissues on embryo performance during germination and the impact of environmental factors on the process. The manuscript represents a solid scientific work which based on usage of numerous experimental methods to draw the conclusions and support the hypothesis. Despite of this, there are some points which have to be improved before the manuscript can be accepted for publication. pp. 5-6 (material and methods), p. 10 and Fig. 2: The major question is concerning the germination assay. The authors should provide how many seeds and replications they used to show inhibitory effect of seed exudates and pericarp extracts on germination of the seeds under study. Similarly, it is not enough to show the inhibitory effect by pictures. Quantification of germination with appropriate statistic processing will have more power of evidence and improve the manuscript. p. 9 and Fig. 1: the authors observed that stressed plants produced equal numbers of pods and seeds per plants as controls but had more aborted seeds. How can it be? Did stressed plants produce more flowers? The authors should clarify this phenomenon. Fig. 1D and E: statistic analysis should be applied to compare germination of stressed seeds in relation to the control seeds. Small remarks and mistakes: P. 6: different font sizes in first and second paragraphs in “Proteome analysis” chapter. P. 13: description of hormones: please use full names with abbreviations in brackets only at first mentions and only abbreviations further in the text. Fig. 7: please use real time (e.g., in hours or minutes) instead numbering for X-axis. This will improve understanding of the figure. After improving, the manuscript can be published in the Journal. Reviewer #2: The manuscript deals with an interesting and important topic in plant reproductive biology with implications for plant growth and development. This is an important and comprehensive work that should eventually be published and will add significantly to the literature. I am a bit concerned by the lack of details in a few areas of methods, and lack of rationale for not having an important treatment, and lack of description of statistics. Kindly address the concerns and resubmit. Line 99-102: They provided the overview of results in the last lines of introduction, while this is common now a days, it would be better to discuss the hypotheses here. Line 107: too vague, where in the desert, what kind of soil, conditions while collecting the seeds? Line 108: What is standard gardening soil? Line 114: Why was the treatment (Heat) by itself excluded? Line 121: This is a bit confusing? Are these self-pollinating flowers? What is the seed set rate and variation among the plants? Without describing the mating system of the species, it is really hard to understand these treatment effects. Line 128 -132: The authors really need to understand what materials and methods mean. This part is designed to provide enough details so others can replicate. No details on how the extraction was done (lyophilizer? Mortar and Pestle, under liq N2?) or details on centrifuge and shaking are provided. Line 136: Sample size? How many seeds per petri dish? When was the germination rate data collected? Line 161; from 4 different plants? A paragraph on statistical analyses and their details needs to be added. It is unlikely that the raw data is normally distributed. So explain what kind of analyses were done and their details. Page 15 and 16: Break it into 2-3 paragraphs. It is extremely tedious to read this, all though everything is relevant and well written. ****** 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.0237045.r001
Revision 1
14 Jul 2020 Author Response Dear Editor, Thanks for the opportunity you granted us to revised our manuscript entitled “Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L. by Khadka et al. We would like to thank the Reviewers for their thoughtful comments. These comments were instrumental in revising and amending our manuscript. Thus the manuscript was modified in light of Reviewers’ comments, which we addressed point by point below. We would like to state that: 1. The manuscript meets PLOS ONE's style requirements 2. Information regarding seed collection was added in M&M. 3. The original uncropped and unadjusted images underlying gel results presented in Fig 4 were included in supplementary information (S6 Fig). 4. All data regarding this study are included in the manuscript and supporting information. Response to Reviewers Reviewer #1: In the proposed manuscript, the authors around G. Grafi have pursued their longstanding research topic to understand the role of dead maternal seed tissues on embryo performance during germination and the impact of environmental factors on the process. The manuscript represents a solid scientific work which based on usage of numerous experimental methods to draw the conclusions and support the hypothesis. Despite of this, there are some points which have to be improved before the manuscript can be accepted for publication. Comment 1: pp. 5-6 (material and methods), p. 10 and Fig. 2: The major question is concerning the germination assay. The authors should provide how many seeds and replications they used to show inhibitory effect of seed exudates and pericarp extracts on germination of the seeds under study. Similarly, it is not enough to show the inhibitory effect by pictures. Quantification of germination with appropriate statistic processing will have more power of evidence and improve the manuscript. Response to comment 1: Details about the germination assays are provided including number of replicates and number of seeds in each replicate (see M&M lines 143-144, and legend to Fig 2). We run more experiments and provided quantification and statistical analysis for the effect of pericarp extracts on germination of B. juncea and S. alba (new Fig 2) Comment 2: p. 9 and Fig. 1: the authors observed that stressed plants produced equal numbers of pods and seeds per plants as controls but had more aborted seeds. How can it be? Did stressed plants produce more flowers? The authors should clarify this phenomenon. Response to comment 2: This data may be confusing, because the data of Fig 1B (Average number of seeds per plant) refers to all seeds produced by a given plant, both normal and aborted seeds (this is noted in the legend to Fig 1). Comment 3: Fig. 1D and E: statistic analysis should be applied to compare germination of stressed seeds in relation to the control seeds.. Response to comment 3: Statistical analysis was added (see Figure 1D and E). Small remarks and mistakes: P. 6: different font sizes in first and second paragraphs in “Proteome analysis” chapter. Font sizes corrected. P. 13: description of hormones: please use full names with abbreviations in brackets only at first mentions and only abbreviations further in the text. Corrected. Fig. 7: please use real time (e.g., in hours or minutes) instead numbering for X-axis. This will improve understanding of the figure. Real time is now provided for the X axis of Fig. 7. After improving, the manuscript can be published in the Journal. Reviewer #2: The manuscript deals with an interesting and important topic in plant reproductive biology with implications for plant growth and development. This is an important and comprehensive work that should eventually be published and will add significantly to the literature. I am a bit concerned by the lack of details in a few areas of methods, and lack of rationale for not having an important treatment, and lack of description of statistics. Kindly address the concerns and resubmit. Comment 1: Line 99-102: They provided the overview of results in the last lines of introduction, while this is common now a days, it would be better to discuss the hypotheses here. Response to comment 1: Hypothesis and the rationale of our study is provided as suggested by the Reviewer (lines 78-82). Comment 2: Line 107: too vague, where in the desert, what kind of soil, conditions while collecting the seeds? Response to comment 2: Details regarding the collection site is provided in M&M (lines 102-105). Comment 3: Line 108: What is standard gardening soil? Response to comment 3: This is a potting soil mixture commonly used in our Institute for growing plants. This soil contains Sphagnum peat moss and perlite (2:1 ratio) supplemented with slow-release fertilizer (5 g/liter) (see lines 105-106). Comment 4: Line 114: Why was the treatment (Heat) by itself excluded? Response to comment 4: We initially attempted to examine certain abiotic stress conditions that prevail in the desert ecosystem during the growing season (winter time) from which seeds were collected. The desert ecosystem is characterized by salty soil, which represents a fixed and continuous stress condition, while heat stress may occur occasionally (usually for a few days) during the growing season (winter time). Thus, we assumed that it would be more relevant to address the effect of limited heat stress when given in combination with salt stress, rather than heat stress alone. Comment 5: Line 121: This is a bit confusing? Are these self-pollinating flowers? What is the seed set rate and variation among the plants? Without describing the mating system of the species, it is really hard to understand these treatment effects. Response to comment 5: Anastatica hierochuntica is a self-pollinating plant. We provided details on its mode of flowering in the text (lines 85-88). Comment 6: Line 128 -132: The authors really need to understand what materials and methods mean. This part is designed to provide enough details so others can replicate. No details on how the extraction was done (lyophilizer? Mortar and Pestle, under liq N2?) or details on centrifuge and shaking are provided. Response to comment 6: We added missing details to the extraction procedure (lines 128-130). Comment 7: Line 136: Sample size? How many seeds per petri dish? When was the germination rate data collected? Response to comment 7: Details on sample size and rate data were added (see legend to Fig. 1 and lines 137-145). Comment 8: Line 161; from 4 different plants? Response to comment 8: Each replicate contains randomly selected seeds or pericarps from a pool of seeds/pericarps of 14-18 plants (see lines 167-169). Comment 9: A paragraph on statistical analyses and their details needs to be added. It is unlikely that the raw data is normally distributed. So explain what kind of analyses were done and their details. Response to comment 9: A paragraph on statistical analyses was added (see lines 265-269). Comment 10: Page 15 and 16: Break it into 2-3 paragraphs. It is extremely tedious to read this, all though everything is relevant and well written. Response to comment 10: Page 15-16 was separated into 3 paragraphs as suggested. Attachments Attachment Submitted filename: 1Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0237045.r002
20 Jul 2020 Decision Letter - Suprasanna Penna, Editor Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L. PONE-D-20-13034R1 Dear Dr. Grafi, 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, Suprasanna Penna Academic Editor PLOS ONE Additional Editor Comments (optional): All the suggestions and comments made by the reviewers have been suitably addressed in the revised version. Comments to the Author Reviewer: 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #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 #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 #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 #2: No https://doi.org/10.1371/journal.pone.0237045.r003
Formally Accepted
22 Jul 2020 Acceptance Letter - Suprasanna Penna, Editor PONE-D-20-13034R1 Maternal environment alters dead pericarp biochemical properties of the desert annual plant Anastatica hierochuntica L. Dear Dr. Grafi: 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. Suprasanna Penna Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0237045.r004

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