Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature

Round 1

Reviewer 1 Report

Introduction

General comment. The introduction feels like a list of facts and not a discussion of why this work is needed. Please provide a better justification for why this work is needed. 

Line 38. Avoid using words like "astonishingly" as these are not scientific and do not add to the overall merit of the paper. Delete "astonishingly" from this sentence.

Line 84. Please provide citation(s) for "high-quality apple genomic data" and "more complete accurate genomic sequences".

Line 85. Make this a new paragraph and please provide clear study objectives and study hypotheses.

Lines 85-93. This paragraph feels more like a repetition of the abstract and less of a discussion of study objectives. Eliminate detailed statements about methods and results and focus on objectives and hypotheses.

Line 94. eliminate the word "solid" as it is not accurate

Materials and Methods

Line 101. Citation 40 is the citation for the genome sequence not for a database.

Lines 109 and 120. Please provide a citation for "the Apple Genome Database" used.

Line 139. What do the authors mean by Fuji seedlings? Are these Fuji open-pollinated seedlings or are these clones? Please clarify in the text.

Lines 140-141. What do the authors mean by "same suitable environment"? Greenhouse conditions? The current sentence is too vague. Please provide sufficient detail.

Line 143. Eliminate "be"

Line 145. How were these sampling times chosen? Based on previous research? Please clarify and provide a citation if needed.

Line 146. Change "irrigation" to "irrigating"

Results

Lines 171-172, 183-184, 218-219, 300-303, 304-305, and 318-320. These are materials and methods statements and do not belong in the results section.

Lines 174-176. This is an unnecessary statement since you already cite the supplementary information in the previous sentence. Remove.

Line 184. Change "are" to "were" to keep consistent.

Lines 194-196, 239-240, and 290-294. These are discussion statements and do not belong in the results section.

Discussion

General comment. The authors tend to use the word "may" when they should be using the word "might". 

Line 349. Insert space before "Identification"

Lines 355-357. This information seems to be addressed in section 4.2. Could these two sections be combined?

Lines 385-386. Could you please provide a supplementary table or figure for readers who are interested in which of the gene pairs show collinearity?

Line 386. Change collinearity to collinear.

Line 410. Change "an important function" to "important functions"

Lines 423-425. This is a very long and confusing sentence. Please revise.

Line 429. Please remove "in the current study" as it adds unnecessary words to the sentence.

Line 430. How was expression altered? Please be more specific in the discussion of your results.

Line 440. I think the authors need to add a paragraph to the discussion that provides a discussion of the overall conclusions and their applications. Answer the questions of what are the overall conclusions? How does this help the scientific community? How can the results be applied? In other words, why should we can and how can we use the results"

 

 

 

 

 

 

 

 

 

 

 

Author Response

Dear Prof.,

We uploaded the word file about the  point-by-point response to the reviewer’s comments to attachment. Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Generally a detailed and exhaustive analysis of the WD40 genes of apple and comparison to Arabidopsis. As well a selection of genes containing WD40 domains were examined to see how they responded to stress. While this is an extension of very similar work to a new species, namely apple, it adds information for a commercial species that is important and will help further transfer of information to apple. An issue is that the function of WD40 proteins is not really known at the cellular and biochemical level, what they are doing, so this paper is a bit of a survey without deeper understanding. Several terms used in analysis of gene duplication are undefined.

 

Specific comments.

Page 2. Reference needed to apple genomic data

Page 3 will the authors justify their use of such low e values (0.01, 0.0001)

Section 2.3. did the authors do a manual check on the predicted expressed genes an predicted proteins?

Section 2.5. the fruit samples also included skin I assume?

Page 3. How were the apples grown for the stress treatment (environmental conditions)? What was the light intensity in the light incubator? How many reps for each treatment? Howmany biological reps for RNA extraction?

Relative gene expression. What housekeeping genes did the authors use for comparison?

Figures 1 to 6 are too small in the printed version and can only be seen clearly in the on line version

Figure 8 shows genes with significant differences. However you don’t refer to the supplementary figures figures 1S to 3S as to what they show

Page 11/12. “The structure of proteins determines their function” is a meaningless statement when you don’t really know the function, let alone the structure

 

 

 

Author Response

Dear Prof.,

We uploaded the word file about the  point-by-point response to the reviewer’s comments to attachment. Please see the attachment.

Author Response File: Author Response.docx

Reviewer 3 Report

This paper presents a study for the identification and characterization of WD40 genes in apple. This category of genes has been previously investigated and shown to be involved in a number of physiological and stress-related processes. The authors started from the identification of genes in the apple genome, followed by a phylogenetic analysis, a sinteny analysis with the corresponding Arabidopsis genes, and expression profiling in different organs and developmental stages. A representative subset of genes was then analyzed for the expression pattern during three different stresses.

This work provides a remarkable amount of information on the localization, structure, phylogeny and function of this class of genes; it can be of great interest to elucidate the molecular mechanisms at the base of different processes in apple. The strategy was correctly set up to address the purpose of the work in every aspect, and the conclusions are correctly deduced from the results. The data are adequately elaborated, interpreted and presented, although some minor changes would help the reader to better understand the information underlying.

The paper is certainly worth of publication; I listed here below some minor modifications which I suggest to improve the final version:

L65: Latin names should be in italics

L143: “were be treated” should be “were treated”

L198-212: I’m not sure that such a description of the different protein subfamilies is useful in the text; it looks a bit redundant. Maybe a simple reference to figures and supplemental materials would be sufficient

L309-311: according to fig. 7, what is written in the text is not exactly true; only MdDW40-17 and -219 are expressed in both roots AND fruits. For the remaining, I suggest to use “OR” instead of “AND”

L334: please briefly explain which genes were down- and which were up-regulated, as for the other two stresses

L349: a space required after “,62].”

L355-357: this is a strong conclusion; were the analysis parameters the same between the analyses conducted on Arabidopsis and rice AND this work?

 

Other remarks:

Figure 3,4,5: I’m aware that these circle plot don’t necessarily provide each single detail of the results, however in my opinion at least the chromosome numbers/names should be readable. Please increase the font size

Figure 6: as above. The font size should be increased

Supplementary file S2: Please relocate plot titles properly

Author Response

Dear Prof.,

We uploaded the word file about the  point-by-point response to the reviewer’s comments to attachment. Please see the attachment.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Introduction

Line 38. Change "an" to "a"

Line 97 Rework sentence because it is not a well written sentence

Line 105 Remove the word "extremely"

Materials and Methods

Line 122 you should cite Jung, S. et al. (2019) 15 years of GDR: New data and functionality in the Genome Database for Rosaceae.  Nucleic Acids Res. 47, D1137-D1145 if you used GDR

Line 136 provide a citation for the Pfam software

Lines 156-162 there are several words in this paragraph that are capitalized that should not be

Line 173 remove the word "of" after irrigating 

Results

Line 215 change "fewest" to "lowest number"

Line 216 change "concentration" to "number"

Lines 329-330 this is a materials and methods statement and does not belong in results

Line 346 this section should be labeled 3.7 not 2.7

Discussion

Line 441 change "may" to "might"

 

Author Response

Please see the attachment.

Author Response File: Author Response.docx