Genome-Wide Identification and Expression Analysis of WRKY Genes during Anthocyanin Biosynthesis in the Mango (Mangifera indica L.)

Round 1

Reviewer 1 Report

Work by Shi  et al on “ Genome-wide identification and expression analysis of WRKY genes during anthocynani accumulation in mango demonstrated” mined 87 mango related WRKY genes. Based on phylogenetic analysis, WRKY genes were divided in to3 groups. Authors also find out cis-acting element responsive for environment stress and plant development. In silico expression   analysis was carried out by SRA data as well validated couples of genes using qRTPCR. Few specific comments are to be clarified:

1.    Otholous and paralogus gene arrangement on mango genome should be provided

2.    Duplication (tandom) events of genes within genome are not provided.

3.    Line 37 to 40 to be rephrased as its too long sentence

4.    Neighbor-joining (NJ) method was used for  building the phylogenetic tree, bootstrap should be 1000 times

5.    Line 143 under Plant materials and treatments- please add the reference for the same

6.    why the intensity of visible and UV-B light were 4000 Lux and 4.5 164 μW•cm-2, chosen?

7.    Wy only three varities of mango were used fo the anthocynanin measurement? Line 167 to lin 168

8.    Clarification is needed for the MM section “Acquisition and analysis of RNA-Seq data” .  not much clarity ? it seems that author hve also done the RNAseq data, if so please add the data analysis part here as well.

9.    Line 224, why MiWRKY16 could not be mapped to any chro- mosome (Figure 3)? Possible reason

10.  Line 377 studies showed that WRKYGQK motif variation might affect the interaction between 378 WKRY and its target genes [53,54]? Add relavant ereference like  Pandey et al. 2018. BMc Genomics  DOI: 10.1186/s12864-018-4506-3

11.  Line 382 make italics of unicellular protist Giardia  lamblia and slime mold Dictyostelium discoideum, contain single WRKY protein with

12.  Suggestion for the “Phylogenetic tree of identified MiWRKY proteins” Fig 1 should have included include WRKY from some other fruit trees

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

The data is sound and the paper is fairly complete.  I have made a few suggestions for the manuscript.  Please see the attachment.

The letters in figures 4 and 5 are difficult to see in the PDF.  Will there be a high resolution version of these figures available in the final manuscript?

File S6 is full of many numbers that are lacking units.  Please note the units in this file.

Comments for author File: Comments.pdf

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

The manuscript number: agriculture-1733244 entitled “Genome-wide identification and expression analysis of WRKY genes during anthocyanin accumulation in mango (Mangifera indica L.)” authored by shi et al., is the cooperative study of transcriptome to find out the involvement of WRKY genes in anthocyanin accumulation in mango. They identified a total of 87 MiWRKY genes and performed their genetic diversity and also analyze the gene expression analysis and anthocyanin accumulation. The reviewer gone through the manuscript and found that the manuscript is presented as per journal guidelines, the contents of the manuscript are in a defined format, table and figures are presented appropriately. The followings are the query and suggestions for improving the quality of the manuscript-

1.      Abstract is more introductory, it may be modified for more results specific, line no. 17- 20 can be modified for better suitability

2.      Delete “many” line no. 18

3.      Replace “development “ with “developmental” line no. 18

4.      Ensure italicize “WRKY and MiWRKY” wherever it is related to transcription factor or gene/s

5.      Replace “hormone” with “hormonal” line no. 25

6.      Replace “a comprehensive” with “comprehensive” line no. 31

7.      Replace “of” with “on” line no. 31

8.      Replace “formation” with “development” line no. 32

9.      Delete “transcription factor” from keywords, the author may add “phylogenetic analysis” for better visibility

10.  Replace “of” with “on” line no. 48

11.  Replace “development processes” with “developmental processes” and delete “including……..and senescence” line no. 52-53

12.  Modify the sentence “Numerous studies have shown that the WRKY TFs are widely involved in the regulation of plant  responses to biotic/abiotic stresses such as bacterial and fungal diseases, insect feeding, wound, drought, low temperature, and salinity [15-17]” as  “Numerous studies have shown that the WRKY TFs are widely involved in the regulation of plant  responses to biotic (bacterial, fungal and insect feeding) and abiotic  (wound,  drought, cold, heat  and salinity [15-17]”

13.  Replace “contributing to the” with “responsible for” line no. 59

14.  Replace “of” with “in” line no. 60

15.  Abbreviate the enzymes within bracket like phenylalanine ammonia-lyase (PAL) throughout the manuscript

16.  Delete “and………structural genes” line no. 65

17.  Modified “development and environment factors” as “developmental stages and environmental factors” line no. 69-70

18.  Delete “including……..fertilizer” line no. 70

19.  Delete “including………potato tuber” line no. 73-74

20.  Check for the “promoter” in line no. 77, I think it should be “promote”

21.  Briefly add a global scenario of mango production, economic importance, and health benefits focusing on anthocyanin

22.  Give attention on italicizing MiWRKY line no. 96, 107, 110 and 112

23.  Replace “including” with “viz. or namely” in line no. 144

24.  Abbreviate “DAFB (Day After Full Bloom)” as Day After Full Bloom “DAFB” line no.151

25.  Replace “darkness” with “dark” line no. 160

26.  Delete “each’ in line no. 169

27.  Method and materials are written nicely but there are many grammatical mistakes that need to be removed

28.  Figure 1 is ok, but in the caption check for italics for gene/s

29.  Figures 2 and 3 are also ok but ensure similar font and font size for all figure

30.  Replace “gene structural” with “gene structure” in line no. 247

31.  Figure 4 is ok, but in the caption check for italics for gene/s

32. Figures 5 and 6 are ok

33.  Figures 7, 8, and 9 are ok

34.  The results were very nicely interpreted in the discussion section but should be more focused on anthocyanin, it is more focused on diversity and there is a need to pay attention to grammatical mistakes and italics of gene/s and plant name/s. The conclusion is ok.

Overall the present manuscript was prepared and presented very nicely, the authors presented huge information in support of their findings. There are very few reports available about WRKYs gene involvement in anthocyanin biosynthesis in mango but there are numerous grammatical mistakes and the use of unscientific words throughout the manuscript. Authors need to pay attention to WRKY transcription factors, WRKY genes, and proteins for italics. 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

"Genome-wide identification and expression analysis of WRKY 2 genes during anthocyanin biosynthesis in mango (Mangifera 3 indica L.)" by shi et al., Authors have done the revision as per suggestions.