Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in ‘duli’ Pear (Pyrus betulifolia Bunge)
, Gang Li 1,†, Jianfeng Xu 1, Qingcui Ma 1, Baoxiu Qi 1,2,* and Yuxing Zhang 1,*Round 1
Reviewer 1 Report
The presented manuscript describes the analysis of genes related to GA signaling in the "duli" pear. The work is well structured and written, and after a few corrections it will be suitable for publication.
Section 2.2 - please make it clear that it is the description of proteins (for which the phylogenetic tree was created), not genes.
Line 132 - the colour used is blue, not “purple”.
Lines 208 and 477- please swap "&" with "and"
Line 248 - the word "Segmental" should be in lowercase
Line 462 - a dot is missing after "et al"
Figures 5 and 7: the font should be larger. Especially the Fig. 7 is illegible, the bars should be wider, and the letters above the bars are not visible at all (if not for the caption, I would not even notice them).
The spaces in front of the square brackets are often missing throughout the work.
Having corrected these minor shortcomings, I think that the manuscript should be published due to its high merit value.
Author Response
Please see the attachment
Author Response File: 
Author Response.docx
Reviewer 2 Report
Very intersting work. Only few changes are required:
Objectievs of the work must be clarified in a separated parragraph without referbnces.
A new section of conlcuisons must be added.
Plant material assyaed must be clarified in the Material and Methods section.
Author Response
Please see the attachment
Author Response File: Author Response.docx
Reviewer 3 Report
Manuscript ID: ijms-1705357
In this ms ID: ijms-1705357, entitled “Genome-wide Analysis of Genes Involved in the GA Signal Transduction Pathway in ‘duli’ Pear (Pyrus betulifolia Bunge)”, the Authors reported and characterized in detail the genes involved in GA signalling in pear ‘duli’ by a combined approach of in silico analysis of the recently sequenced genome of Pyrus betulifolia Bunge and Real Time qPCR experiments. Their work is very interesting, because they provided evidence of the involvement of 15 genes in GA signalling in ‘duli’ pear. Significantly, these data pave the way to further studies on molecular mechanisms of GA signalling in pear.
However, in several points results were not clearly described so the paper has to be revised. English language, typos, and repetitions have also to be checked before publication. This reviewer recommends important revisions of this paper.
Here are some specific comments:
ABSTRACT
L18: remove repetition of “pear”
L23: explain new acronyms
INTRO
L32-33: use plural and introduce acronym GA: “Gibberellin or gibberellic acids (GA)…”; use plural changing “It” to “They” and so on.
L34: add “response” after “stress”
L35: check “then” before “rice”
L42: add SLY
L60: check English in “play overlap yet …”
L74: fix typo in “-Iie-”
L108: fix typo in “DELIA”
RESULTS
L186: remove repetition of “based”
L193, 205: add Figure 3a and 3b
L233: in general, here add the concept of “dispersed” duplication
L253: remove “can”
L257: use “have been” instead of “are”, check “purify”
Par. 2.4: Collinearity is when sets of homologous genes in different species are located on the same chromosome (synteny) and are conserved in the same order. In light of this, the description in L229-333 (Fig. 4a) and L234-241 (Fig. 4b) have to be opportunely changed.
L274: check unicity of cis-elements, HD-zip1 is not the only unique element: GATA-motif etc.
L275-276: it also lacks the GATA-motif
L284: add AT1-motif
L285: use plural “elements”
L290: add 3AF1
L291: add CMA2a
L307: check “reproduction”, should use “hormone response”
Par. 2.6: L317-327 and Figure 6. Here, description of results of relative gene expression have to be opportunely changed, considering a threshold and relative gene expression of 1 indicated no variation. Please, see work of Livack and Schmittgen (2001) available at https://doi.org/10.1006/meth.2001.1262, they reported that the amount of target, normalized to an endogenous reference and relative to a calibrator, is given by the formula: 2−ΔΔCt. Eventually, by using log2(fold change), values are symmetrical and can see fold changes in both directions (+/-). As an important consequence, in your results a significant expression exist only for some tissues, while gene expression level in root is identical (equal to 1) for GIDs, DELLAs, and SLYs.
Par. 2.7: L338-374 and Figure 7. Here, as above, description of results of relative gene expression have to be opportunely changed, considering a threshold and relative gene expression of 1 indicated no variation. Above all in L362-363, they are general trends with some exceptions, this reviewer suggests avoiding net divisions.
L336,376,448: avoid using the term “Altered”, they are only relative physiological responses.
DISCUSSION
L392: add bibliographic reference(s)
L393: check verb tense for “are”
L402: avoid repetitions “duplication doubling”
L412: mis-sequenced ? Please, provide evidence
L416: remove comma
L421: remove “human”
L437: remove the first “important”
L441: use plural for GA
L433: revise expression levels in root and flowers (L320-327)
L450: revise expression levels
L453: remove “was”
L458: change “with” to “of”
L465-480: DELLAs levels are low in roots, revise after Results
L481-482: after revising Results, here revise expression levels
L490-491: rewrite this sentence more clearly
M&M
Add a new paragraph with “Plant material” and introduce the Latin name Pyrus betulifolia Bunge of wild pear
L523: remove repetition of “based”
L500: use “assess” instead of “see”
Conclusions
You have to conclude with main findings and perspectives.
L558: remove this sentence, it is already in the results
L560: write about the applications of the other factors in addition to GA
Author Response
Please see the attachment.
Author Response File: Author Response.docx
Round 2
Reviewer 2 Report
Authoirs have revised correctly the manuscript
