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The authors have addressed all the comments and the manuscript is significantly improved.
[# PeerJ Staff Note - this decision was reviewed and approved by Brenda Oppert, a PeerJ Section Editor covering this Section #]
The Section Editor added:
> The abstract should clarify what they are studying, so I recommend changing these sentences to: "In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT- qPCR)."
In addition to reviewers comments, I have also suggested minor revisions as given below. You shuold address all of these comments.
- In the title, auxinup should be replaced with auxin-up
- Please rephrase “(ⅳ) C: Stem nodes under the treatment of 80% WHC which was the same part of group (iii).
- How did you select the housekeeping gene LrEF1α (JX427553)? Please provide a reference study.
- Please cite the proper study for “The data was quantitated using the 2-ΔΔCt method”
- In the legends of Figure 2, please describe 2a and 2b. Please also add details for legends of other figures.
- Evolutionary tree was constructed using only AtSAURs and LrSAURs. You should also use SAURs from other plants representing different major groups of plants with distinct evolutionary paths. Please also add more details about the results for phylogenetic tree.
- For motif analysis, please mention the importance of motifs in terms of protein structure or function, and which motif is related to domain. In addition, mention the name of protein.
- Please rephrase to mention the identity of heatmaps. “The heatmaps of thorns at different developmental stages in all LrSAURs under drought treatment are shown in Figure 4.”
- Please explain why only 21 SAURs were selected for tissue-specific expression analysis.
Moreover, there are some minor modifications in the manuscript as track changes for your consideration.
Dear Editor,
authors have improved the manuscript in many way possible such as English language and minor corrections.
Most of the corrections authors made in this revised version is they deleted the statements or instances where there is a conflict. However, the comments were mainly to allow them to improve the manuscript.
From their comments, it is understandable that they have no ability to experiment further on the material based on the suggestions made in first round of revision.
At its current stage and content, the manuscript provide basic information on the SAUR family members and their expression trends in used species. So considering the present manuscript, it can be accepted.
see above comments
See above comments
The reviewer comments were addressed and the manuscript could be accepted for publication after the following minor revisions are made.
The grammar of the manuscript has improved. A few points to note:
Line 175: space needed “5.27to”
Up-regulated, down-regulated etc. needs hyphenating
Line 248: Should it read “LrSAURs”?
The comments were addressed. However, I am not sure how the expression levels in Fig, 6 were calculated – were they from qRT-PCR results or from the RNA-seq data? This should be included in the figure legend for clarity.
no comment
no comment
The reviewers have suggested major revisions. You are requested to address all the comments.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
1. No clear and unambigous, professional English was used.
2. Literature is not sufficiently surveyed.
3. Structure is fine.
4. Not self-contained. Authors speculated results in many instances.
1. YES,
2. NO
3. NO.
4. NO.
1. NO - Impact and novelty not assessed. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
2. YES. the data was provided but not rigorously analyzed. All underlying data have been provided; they are robust, statistically sound, & controlled.
3. NO. Conclusions are well stated, linked to original research question & limited to supporting results.
1. Authors claim that it is an economically important shrub (L48). To support this, they should include the relevant data or its input in economy of the said contry.
2. The English language is too complicated and sentence structure is not right on many places. I suggest authors revise their manuscript in terms of language and syntax.
3. In the first para of the intro, authors talk about water/drought stress. is this relevant to this study? By looking at the results it can be seen that authors studied the gene expression under drought stress. However, the limited link between SAUR and drought should be further explored. Also authors should add a separate section of drought stress treatment in the methods.
4. I don’t agree with the following statement “Although SAUR family identification and expression 66 analysis have been conducted in a variety of plants, the functional studies on SAUR are still in the initial stage, and 67 only some family members have been functional analysis”. Multiple SAUR members have been studied and their function is established.
5. Authors should italicize the gene names. At some places they did but not in other places. Be consistent.
6. The introduction section as a whole is too weak and do not represent proper literature survey, lags information, and fails to inform the audience about the known roles of SAURs in hormone signaling and resulting plant traits. Especially they must establish a link between previous knowledge and need for the current study.
7. L81-82. This study can not provide information about biological function unless some of the genes are characterized. Authors should modify this statement.
8. L89. Mention the minor modification.
9. What is the reason for choosing the given L90 concentrations of IAA?
10. The grouping of the samples and their numbering L96-101 is confusing. Carefully check and revise.
11. L111. “Numbered with Lr”?
12. Add dates of access with the links.
13. L156 onwards. It is very strange to present the motif sequences in text. Figure 3 should be supplemented with the seq information of the motifs.
14. Why the authors did not study endogenous IAA content?
15. Authors should discuss their expression results in line with the exogenous application of IAA as well. Does the expression of SUARs increase with increase in IAA or not? Do the SAURs respond differently to different auxin conc in different tissues or growth periods? What does this mean? Is IAA conc negatively or positive related to SAUR expression?
16. Second paragraph of the discussion section does not represent discussion but a literature survey. Authors should discuss how their results are relevant and present novelty.
17. L221-22. How did the authors draw this conclusion? Did they perform any additional analysis to validate it? Just MEME can not validate this. It’s a speculation without validation.
18. L227-232 is just repetition of results. Authors should avoid such instances to repeat the same information in two sections of the manuscript.
19. L240. This is a false claim. The study by Zhang et al., 2017 reported that the expression of SAURs was lower in stem and roots. They did not report that the “number of gene expressed mainly in roots was the lowest”.
20. L246- “We speculated that LrSAUR, which is 247 mainly expressed in stems and thorns, may also be related to the formation and growth of stem thorns.” What are the basis of this “speculation”? Authors must do other sequence characteristics analysis that may support this assumption.
This article is basically written in a good way. It includes all necessary steps covered professionally. In my opinion, in some lines, the sentences were not written in a clear English (For example, line number 67, 71, 77 and 78.
no comment
no comment
This is a first report on SAUR genes in Lycium ruthenicum, which is presented in a very comprehensive way.
This manuscript presents a genome-wide analysis of the SAUR gene family in the Lycium ruthenicum genome and analysed their expression under drought stress. This research could be useful for researchers familiar with this topic and can be used as a platform for further functional validation studies and hypotheses. However, there are some ways that the manuscript can be improved that would make it more useful to the scientific community. This manuscript could be accepted for publication if the appropriate major revisions are made.
1. The grammar needs improving. The manuscript needs revision for grammatical errors and sentence structure, perhaps by a fluent English speaker. For example:
• Line 29: “L. ruthenicum is a thorny shrub that…”
• Lines 32-33: “A total of 33 putative LrSAURs were identified and constructed a phylogenetic tree in L. ruthenicum, they were divided into three clusters.” This sentence needs restructuring.
• Line 36: “21 genes were analyzed by RT-qPCR..” could be changed to “The analysis of 21 genes by RT-qPCR…”
• Line 44: regions
• Line 44: “most of desert plants”
• Line 47-49: needs restructuring
• Line 52: “These findings indicated that…”
• Line 57: “Stem thorns developed from…”
• Line 67: “functional analysis” should be “functionally analysed”.
• Line 68: overexpression of
• Line 80: should a full stop be used instead of a comma?
• Line 90: needs restructuring
• Line 101: needs restructuring. Also, is that the exact name of the sequencing company? I didn’t find any online sequencing companies called Biomarker company, but I found one called Biomarker Technologies Corporation.
• Line 103: “Achieve” should read “Archive”
• Lines 108-110: needs restructuring.
• Line 114: used to analysis analyse
• Line 120: “which” should be “with”
• Line 127: “analysis of…”
• Line 132: “performed with…”
• Line 151: needs restructuring
• Line 152: should be “gene lengths…”
• Line 154: the SI unit for Daltons is Da, not D
• Line 173: needs restructuring
• Line 184: needs restructuring
2. The figure legend for Figure 4 could use some more details. It is unclear what type of expression values are shown (is it raw FPKM or is it normalized and/or log transformed?)
3. The figure legend for Figure 5 (or maybe somewhere in the Methods section) can be labelled to include which conditions these plant samples (root, stem, leaf, thorn) were taken from. Four different planting conditions were described and it is unclear to the reader which one was used for these experiments.
The study seems experimentally sound overall, with the corresponding datasets provided. However, the method could be improved by including:
• A link to the transcriptome database used to obtain the LrSAURs (line 107).
• The methodology used to isolate the RNA and obtain cDNA was not described. If the protocol was previously described, please cite the corresponding article(s).
• For the RNA-seq, was any method used to check the quality of the RNA samples?
• Line 145: You mentioned that there were differences in stem thorns among the different sample conditions. It would be easier for the reader to observe the differences in the amount of thorns in Figure 1 if they were encircled. You also mentioned “significantly higher”. Do you mean significantly taller? Did you take any measurements of the plant and perform statistical analysis on the measurements for each group to determine significane in differences? If you did, this is not mentioned in the methodology.
• The phylogenetic tree would be more informative if it was constructed with SAURs from other species, at least with the A. thaliana SAURs.
• No mention is made in the manuscript of how the raw fastq reads were processed to obtain FPKM values. If an established protocol was used, then this needs to be cited.
• The number of biological replicates were stated for the qRT-PCR experiment. Was this number of replicates also used for the RNA-seq experiment?
The manuscript provides interesting data that could be used for future research on thorn formation during drought stress. However, I have a suggestion that may be useful to improve the validity of the conclusion. While the data shows that SAUR-2, -8, -9, -11, -12, -19 are highly expressed in stems and thorns, it might have also been better to additionally calculate the fold changes from the C and D3 transcriptome samples to see if they were up-regulated during thorn formation induced by drought stress.
Is there a common name thar this plant is commonly referred to as? (Is it black goji berry?). If so, putting the common name in the introduction could help the reader see the importance of this research more easily, since people may not be familiar with the Latin name.
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