Genome-Wide Identification, Characterization, and Expression Analysis under Abiotic Stresses of the UBP Gene Family in Rice (Oryza sativa L.)
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe authors have identified the family of ubiquitin-specific proteases (UBP) in rice. For the 21 selected members, a number of analyses on the gene and protein structure, promoter, syntheny, predictions on protein-protein interactions and gene expression were performed. In addition, the expression of 11 of them was tested using qPCR under certain abiotic stress conditions.
The study provides an initial view on the UBP family and might be helpful for future research. I have a few comments that may help the readability of the manuscript.
Section 3 should read “Results”
Figure 1, the branches of the phylogenetic tree are extremely difficult to see. Please, thicken the lines and make them black. What do the values next to each branch represent? Add this info to the figure legend.
The text in all figures is too small. Consider enlarging the text within the images.
Figure 8, concerning the protein-protein interactions within the UBP family – is this phenomenon known from the literature? It is unclear whether the STRING database only predicts interactions (as stated in Materials and Methods) or does it also list known interactions? Please, state this in the Materials and Methods and in the Results sections.
Among the many proteins potentially interacting with UBP 10, 14 and 22 (Figure 8C-E), only DNA replication helicase 2_4 (OsDNA2_4) was mentioned in Results. What was the reason only this protein to be used as argumentation? A deeper analysis is needed.
Similar to the previous comment, Line 315 – it is unclear based on what criteria 11 UBPs were selected for qPCR analysis.
Author Response
Reviewer #1 (Comments and Suggestions for Authors)
The authors have identified the family of ubiquitin-specific proteases (UBP) in rice. For the 21 selected members, a number of analyses on the gene and protein structure, promoter, syntheny, predictions on protein-protein interactions and gene expression were performed. In addition, the expression of 11 of them was tested using qPCR under certain abiotic stress conditions.
The study provides an initial view on the UBP family and might be helpful for future research. I have a few comments that may help the readability of the manuscript.
- Section 3 should read “Results”
Response: Thank you for pointing out the error. We have modified as your suggestion in line 143 and highlighted it in yellow.
- Figure 1, the branches of the phylogenetic tree are extremely difficult to see. Please, thicken the lines and make them black. What do the values next to each branch represent? Add this info to the figure legend.
Response: Thanks for your suggestion. The branch lines of the phylogenetic tree have been thickened. The values next to branches represent the bootstrap. We have added the illustration in Figure 1 legend in line 163. The relevant texts have been highlighted in yellow.
- The text in all figures is too small. Consider enlarging the text within the images.
Response: We completely agree with your suggestion. The text within the images have enlarged in all figures.
- Figure 8, concerning the protein-protein interactions within the UBP family – is this phenomenon known from the literature? It is unclear whether the STRING database only predicts interactions (as stated in Materials and Methods) or does it also list known interactions? Please, state this in the Materials and Methods and in the Results sections.
Response: Thanks for your constructive question. Currently, there are no literature reports that OsUBP family members interact with each other. In this study, the protein-protein interactions within the OsUBP family are predicted by uploading OsUBP protein sequences to the STRING database (https://cn.string-db.org/). Edges in PPIs network represent protein-protein associations. Associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function, but this does not necessarily mean they are physically binding to each other.
In the STRING database, predicted functional partners include known interactions, predicted interactions and others, which are classified based on the source of evidence suggesting a functional link. The sources of evidence for known interactions include experimentally determined, from curated databases. The sources of evidence for predicted interactions include gene neighborhood, gene fusions and gene co-occurrence. The sources of evidence for others include textmining, co-expression, protein homology. We have added the illustration in Materials and Methods in line 123. The sources of evidence are shown in Figure 8 and illustrated in Figure 8 legend in line 284. The relevant results have further been stated in the Results section in line 265-273. The relevant texts are highlighted in yellow.
- Among the many proteins potentially interacting with UBP 10, 14 and 22 (Figure 8C-E), only DNA replication helicase 2_4 (OsDNA2_4) was mentioned in Results. What was the reason only this protein to be used as argumentation? A deeper analysis is needed.
Response: Thank you for your suggestion. We mainly focus on proteins related to abiotic stresses in this study. According to the descriptive information of all interaction proteins, there are two interaction proteins related to abiotic stresses. As you suggestion, it is not appropriate to only mention one protein related to abiotic stresses in the Results. Therefore, we have supplemented abiotic stress-related protein in the Results in line 268. The relevant texts are highlighted in yellow.
- Similar to the previous comment, Line 315 – it is unclear based on what criteria 11 UBPs were selected for qPCR analysis.
Response: Thanks for your suggestion. The criteria have been supplemented in Results in line 329. The relevant texts are highlighted in yellow.
Reviewer 2 Report
Comments and Suggestions for AuthorsIn the present manuscript, authors have identified and characterized the UBP gene family in rice for their role in abiotic stress response. They identified 21 UBP genes and characterized by in silico approaches and their expression was studied in response to different abiotic stresses. The study is important, and the manuscript is well written. If possible, change the colors of groups in Figure 1 as some of the colors are not properly visible, especially the name of the groups is not visible in figure. The quality of all the figures needs to be improved. The labels/names in the figure are not clear. The titles of the figures (Fig. 8, 9,10) should be given below the figure. It is confusing in the manuscript.
There are some minor typographical or grammatical mistakes that need to be taken care of. The other minor comments are as below.
Line 39: delete “have to” and add “has”
Line 69: Correct the gene name “BnaUBP15”
Line 107: replace “downloading” with “downloaded”
Line 110: correct the sentence as “The chromosomal positions of OsUBP genes were obtained according”
Line 190: Delete the word “genome”. Its not genome sequence, its only sequence or nucleotide sequence.
Line 395: replace “previously” with “previous”
Comments on the Quality of English LanguageThere are some minor typographical or grammatical mistakes that need to be taken care of. The other minor comments are as below.
Author Response
Reviewer #2 (Comments and Suggestions for Authors)
- In the present manuscript, authors have identified and characterized the UBP gene family in rice for their role in abiotic stress response. They identified 21 UBP genes and characterized by in silico approaches and their expression was studied in response to different abiotic stresses. The study is important, and the manuscript is well written. If possible, change the colors of groups in Figure 1 as some of the colors are not properly visible, especially the name of the groups is not visible in figure. The quality of all the figures needs to be improved. The labels/names in the figure are not clear. The titles of the figures (Fig. 8, 9,10) should be given below the figure. It is confusing in the manuscript.
Response: Thanks for your review and suggestion. The colors of groups in Figure 1 have been deepened. The colors of the groups name have been changed to ensure visibility. The text within the images have been enlarged in all figures. The titles of the all figures also have been given below the figures.
There are some minor typographical or grammatical mistakes that need to be taken care of. The other minor comments are as below.
- Line 39: delete “have to” and add “has”
Response: Thank you for your careful check. We have modified as your suggestion in line 39 and highlighted it in yellow.
- Line 69: Correct the gene name “BnaUBP15”
Response: Thank you for your careful check. We have modified as your suggestion in line 69 and highlighted it in yellow.
- Line 107: replace “downloading” with “downloaded”
Response: Thank you for your careful check. We have modified as your suggestion in line 107 and highlighted it in yellow.
- Line 110: correct the sentence as “The chromosomal positions of OsUBP genes were obtained according”
Response: Thank you for your careful check. We have revised this sentence in line 110 and highlighted it in yellow.
- Line 190: Delete the word “genome”. Its not genome sequence, its only sequence or nucleotide sequence.
Response: Thank you for pointing out the mistakes and popularizing professional knowledge. We have deleted the word “genome” in line 192.
- Line 395: replace “previously” with “previous”
Response: Thank you for your careful check. We have revised “previously” with “previous” in line 412 and highlighted it in yellow.
