Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity

Michael Schneider; Lucia Vedder; Benedict Chijioke Oyiga; Boby Mathew; Heiko Schoof; Jens Léon; Ali Ahmad Naz

doi:10.1371/journal.pone.0265981

Peer Review History

Original SubmissionMarch 10, 2022
16 May 2022 Decision Letter - Raffaella Balestrini, Editor PONE-D-22-07169Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivityPLOS ONE Dear Dr. Schneider, 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 30 2022 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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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. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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: Partly ******** 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 by Schneider et al. deals with global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8 h) The application of a short photoperiod regime resulted in gene expression variations between tissues and species. In particular, in the functional analysis, the intraspecies comparison revealed a generally lower expression of genes in barley tissues than tomato. The research could be interesting for the agricultural field in the face of the climate change, however the manuscript appears to be too descriptive due to the lack of multi-disciplinarity. The results obtained with the MACE approach and subsequent bioinformatic analyses are quite interesting, however no other methods were used to substantiate these data. I would expect some morphological and biochemical data along with transcriptomics. The effects due to short-day conditions should be visible also at morphological and biochemical level. Moreover, I think that a validation of the MACE analysis should be carried out, maybe by analyzing the expression of some identified and selected genes by qPCR. Finally, I could not find example of specific genes differentially expressed in GO categories. Only a general description is provided. The authors should also report some specific gene name and number. Fig 2 D. I’m surprised to read “vasoactive intestinal polypeptide receptor activity”. Can the authors give an explanation? Materials and Methods Authors should report some additional details about the humidity level in the growth chamber. This parameter is missing The manuscript contains a number of typographical errors that will require to be corrected. Authors should check carefully the text and correct all the English mistakes. I would also use the term orthologous genes instead than ortholog genes. ****** 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.0265981.r001
Revision 1
13 Jul 2022 Author Response >>>>The research could be interesting for the agricultural field in the face of the climate change, however the manuscript appears to be too descriptive due to the lack of multi-disciplinarity. The results obtained with the MACE approach and subsequent bioinformatic analyses are quite interesting, however no other methods were used to substantiate these data. I would expect some morphological and biochemical data along with transcriptomics. The effects due to short-day conditions should be visible also at morphological and biochemical level. A: We thank the reviewer for this suggestion. To accommodate this idea, we additionally performed an experiment on the photosystem II activity und short (8h) and long day (16h) conditions in a growth chamber. The settings were described in the manuscript, l.155-164. As previously reported in the manuscript, we observed a variant expression of the photosystem II in barley and tomato shoot tissues. Therefore, we set up the hypothesis that such variations in expression should result in measurable differences in the relative chlorophyll content of the leaves. Furthermore, we hypothesized that the relative chlorophyll content should • not be different between tomato plants grown under 8h and 16h daylength conditions • should be different between barley plants grown under 8h and 16h daylength conditions • be higher in tomato compared to barley leaves under 8h conditions. We tested these hypotheses by measuring the relative chlorophyll content in the oldest and youngest leaf to the end of the daylight phase and found evidence supporting all our hypotheses (line 317-325, line 429-448). >>>>Moreover, I think that a validation of the MACE analysis should be carried out, maybe by analyzing the expression of some identified and selected genes by qPCR. A: We had considered performing qPCR studies to validate some of our gene-expression findings. But based on the fact that (I) all three biological replicates showed a striking high expression correlation and (II) previous studies had shown close correlations between qPCR and RNAseq data (1–5), we decided to eschew those experiments. >>>>Finally, I could not find example of specific genes differentially expressed in GO categories. Only a general description is provided. The authors should also report some specific gene name and number. A: Thank you for this suggestion. We included for some selected GO categories the number of genes, name, and function of selected genes (line 237pp, line 245pp, line 283pp). If a reader is more interested in finding information on all gene expressions and the responding category (GO), a reader can have a look at the supplementary tables. We tried to improve the readability of these tables as well. We hope the performed changes are in line with your expectations. >>>>Fig 2 D. I'm surprised to read "vasoactive intestinal polypeptide receptor activity". Can the authors give an explanation? A: We thank the reviewer for this valuable comment. We dissected our data and found six genes associated with this gene ontology (GO:0004999). While the average normalized gene expression was 364 reads in the tomato root meristem across all those six genes, on average 4 reads were examined for the shoot meristem. One additional important fact we realized when dissecting the data was that all six genes were also associated with the DNA binding GO term GO:0003677. As the vasoactive intestinal polypeptide receptor activity seems to you and to us to be an unlikely candidate class, we changed the naming in the figure accordingly to DNA binding. We thank you for mentioning this aspect and for improving our manuscript with this comment. >>>>Authors should report some additional details about the humidity level in the growth chamber. This parameter is missing A: We added this detail in line 80. >>>>The manuscript contains a number of typographical errors that will require to be corrected. Authors should check carefully the text and correct all the English mistakes. I would also use the term orthologous genes instead than ortholog genes. A: We revised the manuscript another time to rule out language-related errors. As you may notice, we have tried our best to address the concerns of reviewer 1. We are grateful to the reviewers and the editor for the time, efforts, and valuable suggestions that resulted in a better manuscript. References: 1. Shi Y, He M. Differential gene expression identified by RNA-Seq and qPCR in two sizes of pearl oyster (Pinctada fucata). Gene. 2014 Apr 1;538(2):313–22. 2. Wu AR, Neff NF, Kalisky T, Dalerba P, Treutlein B, Rothenberg ME, et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods 2013 111 [Internet]. 2013 Oct 20 [cited 2022 Jun 17];11(1):41–6. Available from: https://www.nature.com/articles/nmeth.2694 3. Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, et al. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics [Internet]. 2009 Nov 16 [cited 2022 Jun 17];10(1):531. Available from: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-531 4. Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, et al. Alternative expression analysis by RNA sequencing. Nat Methods 2010 710 [Internet]. 2010 Sep 12 [cited 2022 Jun 17];7(10):843–7. Available from: https://www.nature.com/articles/nmeth.1503 5. Everaert C, Luypaert M, Maag JLV, Cheng QX, DInger ME, Hellemans J, et al. Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data. Sci Reports 2017 71 [Internet]. 2017 May 8 [cited 2022 Jun 17];7(1):1–11. Available from: https://www.nature.com/articles/s41598-017-01617-3 Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265981.r002
18 Aug 2022 Decision Letter - Raffaella Balestrini, Editor Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity PONE-D-22-07169R1 Dear Dr. Schneider, 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, Raffaella Balestrini 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: The manuscript has been improved and the authors made all the corrections/modifications according to my suggestions. ****** 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.0265981.r003
Formally Accepted
2 Sep 2022 Acceptance Letter - Raffaella Balestrini, Editor PONE-D-22-07169R1 Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity Dear Dr. Schneider: 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 Raffaella Balestrini Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265981.r004

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