The Auxin/Indole-3-Acetic Acid (Aux/IAA) Gene Family Analysis of Four Rosaceae Genomes and Expression Patterns of PmIAAs in Prunus mume
Round 1
Reviewer 1 Report
In the article “The auxin/indole-3-acetic acid (Aux/IAA) gene family analysis of four Rosaceae genomes and screening PmIAAs involved in floral scent synthesis in Prunus mume” by Liu et al., the authors studied the AUX/IAA family in Prunus. I think it is a good article, however I think that there are some major and minor issues. My main doubt is that I don’t think the authors shows enough evidence to suggest that some AUX/IAA and involved in floral scent synthesis in Prunus mume. The only information comes from RNAseq data in P. mume. Moreover, the authors highlight that only P. mume emits flower scent. However, no data is shown that compares the gene expression level of PmIAA 2 and 15 during flower development in P. persica, P. dulcis and P. armeniaca. Without this comparison there is no link that supports the author statement.
For the minor points, please find bellow the specific comments:
The English needs a lot of editing.
line 35-37: I think that the canonical auxin signaling needs to be introduced. The authors only explain Aux/IAA and this information is key to understand their relevance in auxin signaling.
line 134: PaIAA1-16-f is not really clear. Should be 33. Maybe put (a-f)
Line 144: this is from RNA or aminoacid sequence?
line 150: check grammar
line 171: motifs 1-10? How this correlates with the known I-IV domains?
Fig 3: Maybe is better to show all chromosomes in the figure and not just the one with AUX/IAA
Line 256: Not sure about this statement. This is evident only for PmIAA3
Line 264: To my knowledge, auxin is a key component of flower development. Thus, the expression in flower is not exclusively related with secondary metabolism.
Line 268-270: I agree, but what about PmIAA16 and perhaps also PmIAA17? These genes also show a similar trend with a maximum expression in FS and decreasing in WS.
Author Response
Please see the attachment.
Author Response File: 
Author Response.docx
Reviewer 2 Report
In the manuscript "The auxin/indole-3-acetic acid (Aux/IAA) gene family analysis 2 of four Rosaceae genomes and screening PmIAAs involved in 3 floral scent synthesis in Prunus mume' authors elaborated on the role of gene families related to auxin in prunus mume. this study will be helpful for readers and have interesting findings, however, the MS needs to address the following concerns
Abstract: Line 13-14 I would suggest to remove and adding technical and meaningful sentences
"108 RoIAAs were distributed in chromosomes 19 unevenly." sentences are not well connected
Line 21-23 rephrase results in accordance with data
Introduction: elaborate the importance of Prunus mume and auxin/indole-3-acetic acid
Results: 3.1. I would suggest rewriting, fig/supporting data tables are not cited
168-169 what is the number of motifs ?? "The similar motifs were observed in 168 these RoIAAs that were in the same group."
"four Rosaceae plants" is a bit difficult to understand for readers, better to mention the name of the Plants
Line 281 mentions how many cis-acting elements were detected by PlantCARE database
Discussion: line 300, little comprehensive bioinformation analysis??
Line 323-333 include review and discussion
Line 365 this section should include a conclusion based on your findings
Figures: Figures 1 & 8 legends should be self-explanatory
Author Response
Thank you for your comments concerning our manuscript entitled “The auxin/indole-3-acetic acid (Aux/IAA) gene family analysis of four Rosaceae genomes and screening PmIAAs involved in floral scent synthesis in Prunus mume” (horticulturae-1880328). And these comments are valuable and very helpful for us to revise and improve this manuscript.
Point 1: Abstract: Line 13-14 I would suggest to remove and adding technical and meaningful sentences "
Response 1: We appreciated this suggestion. We had improved it in the abstract part. Please refer to the lines 12-18. Hope it is meaningful.
Revise: Floral scent is a significant character in ornamental plants and consists of a blend of volatile or-ganic compounds with low molecular weight. It has been reported that Aux/IAA proteins play vital roles in floral volatiles metabolism in many plants. Prunus mume emits pleasant floral scents distinguished with other species in Prunus of Rosaceae. However, there was few of studies on the Aux/IAA gene family in Prunus plants in Rosaceae and their roles in floral scent synthesis in P. mume.
Point 2: 108 RoIAAs were distributed in chromosomes 19 unevenly." sentences are not well connected.
Response 2: The sentences "108 RoIAAs were distributed in chromosomes 19 unevenly." was changed to “However, the physical distributions of RoIAAs on chromosomes of every species showed completely uneven” in lines 24-25. Hope it is suitable.
Point 3: Line 21-23 rephrase results in accordance with data
Response 3: We sincerely apologize for this. The error has been fixed in accordance with the date in Table 2. “four pairs of PaIAAs” has been revised to “three pairs of PaIAAs” in line 26.
Point 4: Introduction: elaborate the importance of Prunus mume and auxin/indole-3-acetic acid.
Response 4: As you suggested, we implied the importance in Prunus mume in line 71. The importance of auxin and the auxin signaling have been introduced in lines 47-51. Please check it.
Point 5: Results: 3.1. I would suggest rewriting, fig/supporting data tables are not cited.
Response 5: We sincerely apologize for this. As you suggested, we have revised the result 3.1 and cited table 1 relevantly. The supplementary tables were cited in the corresponding place in the manuscript in lines 181 (Table S1) and 262 (Table S2).
Point 6: 168-169 what is the number of motifs ?? "The similar motifs were observed in 168 these RoIAAs that were in the same group."
Response 6: As your comment, we have provided the specific numbers of motif and we think it is more appropriate in the explanation in line 198-200.
Point 7: "four Rosaceae plants" is a bit difficult to understand for readers, better to mention the name of the Plants.
Response 7: We agree and have updated. The simple statement “four Rosaceae plants” has been revised to “P. mume, P. persica, P. dulcis and P. armeniaca” in line 84, 170, 177, 215, 251, and 414.
Point 8: Line 281 mentions how many cis-acting elements were detected by PlantCARE database.
Response 8: Thank you for your suggestion. ‘several cis-acting elements’ has been revised to ‘nineteen cis-acting elements’ in line 324. Please check it.
Point 9: Discussion: line 300, little comprehensive bioinformation analysis??
Response 9: Thanks for your reminder. There were many reports that on bioinformation analysis of Aux/IAA genes family in other plants. While there were a few of reports on bioinformation analysis of Aux/IAA genes family in Prunus plants in Rosaceae. We have improved the statement in lines 345-346.
Point 10: line 323-333 include review and discussion
Response 10: As your comment, we have simplified the review to highlight the discussion in PmIAAs and revised the disscussion section in in lines 370-380, hope it is proper.
Point 11: Line 365 this section should include a conclusion based on your findings
Response 11: We appreciate your suggestion and agree with you. According to your suggestion, the findings “Expression analysis implies that PmIAA2, PmIAA15, PmIAA9 and PmIAA10 shows a fluctuating trend was in consistent with floral volatiles emitting generally. And these selective genes might play important roles in floral aroma formation.” have been added in the lines 416-418 in the section.
Point 12: Figures: Figures 1 & 8 legends should be self-explanatory
Response 12: Inspired by your suggestion, we have made the changes. The legends would explain the figures 1 & 8 in more details. And we also revised other figure legends. Please refer to the revised version.
Round 2
Reviewer 1 Report
In the revised article “The auxin/indole-3-acetic acid (Aux/IAA) gene family analysis of four Rosaceae genomes and screening PmIAAs involved in floral scent synthesis in Prunus mume” by Liu et al., the authors addressed most of the comments. The English improved considerably, now it reads better. However, still it needs more work before publication. Also, other comments such as the description of the auxin signaling pathway in the introduction and other minor points in the results were resolved.
Regarding my major issue in the previous revision, I have to insist in. The authors argue that the RNAseq data used in this work was reliable, that was not the point. I do not have any doubt about the robustness of the data. Also, it has been studied that flower scent is a key characteristic in P. mume. This has been characterized by Hao et al., 2014 as pointed out and more recently by Wang et al., 2021 (https://doi.org/10.3390/molecules26237256). The link between auxin signaling and flower scent has been studied by Ke et al., 2019 (as pointed out by the authors) and also by Orlova et al., 2006 in Petunia flowers (www.plantcell.org/cgi/doi/10.1105/tpc.106.046227). Orlova et al showed that RNAi plants for an ALCOHOL/PHENYLETHANOL BENZOYLTRANSFERASE (BPBT) gene affects flower scent metabolites. Interestingly it also alters flower morphology and auxin transport. On the other hand, Ke et al., 2019 studied the AUX/IAA family related to flower scent in Hedychium coronarium. However, the authors not only selected AUX/IAA genes based on transcript abundance during flower development. Ke et al. used “Transcript abundance in flower organs; high expression in the labellum and lateral staminode, which are the main parts that emit floral scent; responsiveness to IAA and PCIB, which significantly influence flower scent formation; and expression patterns during flower developmental stages that match the emission of volatile compounds” to select the AUX/IAA. Moreover, Ke et al. validated 2 of these genes by virus-induced gene silencing (VIGS) to silence HcIAA2 and 4 and confirm this link. In contrast, the authors in this article only have 7 lines (309-315) in the result section that are dedicated to make a link with flower scent. Moreover, this was not validated by qPCR or compared with the other Prunus species. Thus, I still believe that the authors do not provide enough evidence to support that the AUX/IAA selected in this study are indeed related to flower scent. I think that the link between the AUX/IAA and flower scent should be tunned down. I strongly suggest to change this in the tittle as well. Can be part of the paper as a section of the results but I am not convinced that the authors have enough evidence to put that statement. Moreover, please include the papers mentioned above (Wang et al., 2021 and Orlova et al., 2006), I think it is relevant. Particularly because the link between the metabolites responsible for flower scent/flower development/auxin can be discussed.
Minor comments
English improved considerably. However, there are a lot of grammar mistakes that should be addressed before publication.
63-65: In flowers?
67-68: Based on the evidence point out, in secondary metabolites and possibly flower scents. The work done by Orlova et al., 2006 should be included to better support this point.
165: Considering that in Hedychium coronarium it has been characterized the role of HcIAA2 and 4, it will be ideal to include at least those genes in the analysis.
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 3
Reviewer 1 Report
All comments and suggestions has been addressed.
