Genome-Wide Identification and Expression Analysis of the PME and PMEI Gene Families in Diospyros kaki: A Bioinformatics Study

Round 1

Reviewer 1 Report

L12- Pectins is the major components of cell walls in plants, - Punctuation- insert a full stop instead of a comma. The sentence has a mixture of both plural and single tense, please rectify

 

L17 Similar and not Similarity, rectify

 

 

 1. Introduction

L33…….…. form of pectic? synthesized…… insert is where there is ? to make the statement complete

L35 Pectin methylesterase inhibitor (PMEI) inhibits and not inhibited

L49 …………Identified in multiple plants7. Delete 7or if its is a citation, please have it well cited.

L52 ………have been identified. Delete this after the citation

L61 ………………East Asia36 if 36 is a citation, then correct it.

 

3. Results

Figure 2 Could you please distinguish which is figure and b. in the present state, its not easy to distinguish a and b.

 

Figure 3 Could you please distinguish which is figure and b. in the present state, its not easy to distinguish a and b.

L194 The duplication analysis showed that 2 and 2 DkPME… please expound on this sentence. What does the 2 highlighted in red represent?

 

Figure 4 Chromosome location of DkPME genes in D. kaki. Genes of different groups are expressed in different colors. Blue dashed lines showed fragment duplication events, and gray boxes presented tandem duplication events. The blue dashed lines could not be seen

 

L24 The PME and PMEI gene families are involved in cell wall modifications,

 

Thus, we inferred that the PME and PMEI genes were conservation between persimmon species but might show high inter-species polymorphism. Consider changing highlighted word to conserved

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Dear Authors,

 

Reviewer comments Horticulturae-2059784

The manuscript entitled „Genome-wide idenfication and expression analysis of the PME and PMEI gene families in Diospyros kaki“ represents a useful bioinformatics study aimed at an investigation of DkPME and DkPMEI families in Diospyros kaki involved in pektin biosynthesis and pectin biosynthesis modulation, respectively. The authors provided bioinformatics analysis of DkPME and DkPMEI genes based on the published Diospyros kaki genome and aanalysed PME and PMEI gene structure, phylogeny, cis-elements, and expression based on the published transcriptomic data.

I think that the present manuscript provides a useful study on D. kaki PME and PMEI genes and thus is useful for publication in Horticulturae.

I have only a few minor formal comments on the present manuscript which are given below:

Manuscript title: I think that the fact that the present manuscript is a bioinformatics study utilizing publicly available data should be indicated in the manuscript title which should be modified as follows: „Genome-wide identification and expression analysis of the PME and PMEI gene families in Diospyros kaki: a bioinformatics study“.

Abstract, line 12: Use a plural form of the verb in the statement: „Pectins are the major components of cell walls in plants,…“

Abstract, line 17: Modify the statement as follows: „…which indicates the function of these DkPME/DkPMEI were similar.“

Abstract, line 17: Correct the typing error in the word „Besides,…“ (not „Beisdes“).

Abstract, line 22: Add a comma both before and after the word „respectively“ in the statement „…that DkPMEI21 and DkPMEI15 were core nodes and were, respectively, a positive and a negative regulator for carbohydrate metabolism stress responses…“

Introduction, line 33: Use the word form „The richest formo f pectin synthesized in the Golgi apparatus…“ instead of „the most rich form“. What is the richest form of pectin??  Maybe the whole statement has to be modified such as follows: „…and rhamnogalacturonan-II (RG-II) the richest form of pectin synthesized in the Golgi apparatus with a highly methyl-esterified state.“

Introduction, line 36: Add a space between the word „plants“ and the following reference „[6].“

Introduction, line 72: Use the term „…and in silico expression analysis…“ (not „silico expression analysis“).

Introduction, line 75: Modify the statement as follows: „…and the role of DkPME and DkPMEI gene sin persimmon fruit development.“

Materials and methods, line 80: In addition to the reference on the persimmon genome „NCBI Sequence Read Archive PRJNA810977“, the date of access to persimmon genome data has to be added.

Results, Figure 1, line 149: Add a space between „Figure“ and „1“.

Results, line 188: Modify the statement as follows: „DkPME and DkPMEI genes were identified in 13 and 9 of 15 D. kaki chromosomes, respectively (Table S1, Figures 4 and 5).“

Line 190: Add a comma both before and after the word „respectively“.

Line 201: The term „MYA“ has to be explained when used for the first time:  „million years….???.

Results, line 212: Add a space between „A. thaliana“ and „[21].“

Discussion, line 250: Replace the word „less“ with „lower“ in the statement „The number of PMEs and PMEIs in persimmon was lower than that in A. thaliana which might be associated with…“

Discussion, line 271: Modify the word form „were conservation“ to „were conserved“ in the statement „Thus, we inferred that the PME and PMEI genes were conserved between persimmon species…“

Line 284: Add a space between the words „C. sinensis“ and „[54]“.

Line 290: Add a comma following the words „in persimmon,….“

 

Final recommendation: Accept after a minor revision.

 

 

Comments for author File: Comments.pdf

Author Response

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Author Response File: Author Response.pdf