Genome-Wide Analysis of MIKCC-Type MADS-Box Genes Reveals Their Involvement in Flower Development in Malus Lineage
Round 1
Reviewer 1 Report
Dear Authors,
reviewing such interesting and well-conducted studies and well-prepared manuscript as this one entitled "Genome-wide analysis of MIKCC-type MADS-box genes reveals their involvement in flower development in Malus lineage" by Kun Ning, Wang Zhang, Dong Zhang, Yousry A. El-Kassaby and Ting Zhou, it's a real pleasure.
The Authors of this manuscript, based on the conserved domains of MIKCC-type MADS-box gene family, identified 341 genes among 13 genome-released species distributed in Chlorophyta, Bryophyta, Lycopodiophyta and Magnoliophyta. And as a result of their research, they provided new information on the development of flowers in the genus Malus.
I believe that the subject of the research is interesting, and the goal set by the Authors has been achieved. In the Introduction chapter, there is a proper introduction to the subject of research. Methodologically, the research is well conducted and properly presented in the Materials and Methods chapter. Discussion and Conclusion meet my expectations as a scientific publication. I only have a few minor comments that will allow the Authors to further improve this manuscript.
My comments are below:
1) Keywords should not duplicate words appearing in the title of the manuscript. Also, please put your keywords in alphabetical order.
2) Abstract - please briefly and concisely summarize the research hypothesis.
3) Lines 88-91 - should the scientific names of species not be in italics.
4) Figure 1 - I don't understand why this graph is completely illegible?
5) Figure 4 - please explain what I and II and A, B, and C Class mean. My request stems from the principle that all figures and tables in publications should be understandable without the need to look for explanations of abbreviations elsewhere in the publication.
In conclusion, I believe that the manuscript is of high scientific value and is well prepared in terms of content and technology. Therefore, I believe that the Editorial Board of the Horticulturae journal should consider publishing this manuscript.
Author Response
1）Keywords should not duplicate words appearing in the title of the manuscript.Also, please put your keywords in alphabetical order.
We thank the reviewer for pointing out this issue. We have changed the keywords and put them in alphabetical order.
2）Abstract - please briefly and concisely summarize the research hypothesis.
Thanks for giving me your suggestion. We have rewrited the research hypothesis. MIKCC-type MADS-box genes are involved in floral organ identity determination but remain less studied in Malus lineage.
3) Lines 88-91 - should the scientific names of species not be in italics.
Thanks for giving me your suggestion. In fact, according to the International Code of Botanical Nomenclature, the generic and species names in the scientific names of species must be written in italics.
4）Figure 1 - I don't understand why this graph is completely illegible?
We apologize for the unclear graph, due to the evolutionary relationship of 341 target MADS-box genes, the actual size of figure is relatively large. So, we have rearranged Figure 1, truncated the original figure, put I group on the left, and the II and III groups on the right.
5）Figure 4 - please explain what I and II and A, B, and C Class mean.My request stems from the principle that all figures and tables in publications should be understandable without the need to look for explanations of abbreviations elsewhere in the publication.
Thanks for giving me your suggestion. A, B, and C-Class mean A-class, B-class and C-class MIKCC-type MADS-box genes in the ABC model, respectively. While, I and II mean different evolutionary sub-branches.
Reviewer 2 Report
In this study, the authors conducted genome-wide analyses of MIKC-type MADS-box genes in 13 plant species and performed phylogenetic analyses using the identified genes. They also examined the comparative analysis of MIKC-type MADS-box gene families between Arabidopsis and Malus species, and revealed whole genome duplication and tandem duplication events of MIKC-type MADS-box genes in the Malus genus. The manuscript is nicely written and the authors conducted extensive bioinformatic analyses, presenting some interesting results. However, some revisions are suggested.
The title should be changed to "Genome-wide analyses of MIKCC-type MADS-box genes in 13 plant species."
The abstract should be written up to 200 words and should begin by describing the general role of MADS box genes in plants.
In the materials and methods, please indicate the accession dates for the databases and programs used in this study.
Please italicize scientific names in L88-94.
In L147-148, indicate the threshold for differentially expressed genes using the DESeq2 program. Figure 1 is too small, so please display a simplified version indicating the number of genes in each group in the manuscript.
The original Figure 1 can be moved to Supplementary Figure 1.
Figure 2 can be reorganized, for example, by placing A on the upper panel and B, C, and D on the bottom panel.
In Figure 4, please show one heatmap instead of two heatmaps in one column, and the legend of Figure 4 should describe the colors used in the heatmaps.
In L300-327, it is important to describe how the authors obtained DEGs; if FPKM or TPM values were used in the heatmap, please provide details.
Author Response
1）The title should be changed to "Genome-wide analyses of MIKCC-type MADS-box genes in 13 plant species."
We respectfully disagree. This article does analyze the MIKCC-type MADS-box genes in 13 plant species, but this is only a small part of the groundwork. We focus on comparing the evolution relationship of MIKCC-type MADS-box genes related to ABC flower development in Arabidopsis thaliana and Malus species, and analyzing the gene expression profiling of 18 different Malus domestica cultivars and in 10 different stages of flowering development. So, I think “Genome-wide analyses of MIKCC-type MADS-box genes in 13 plant species” can not comprehensive enough reflect these researches.
2）The abstract should be written up to 200 words and should begin by describing the general role of MADS box genes in plants.
Thanks for giving me your suggestion. We have rerefined the abstract.
3）In the materials and methods, please indicate the accession dates for the databases and programs used in this study.
Thanks for giving me your suggestion. We have added accession dates in the method section.
4）Please italicize scientific names in L88-94.
We agree with this suggestion and have changed the scientific name of species in italics.
5）In L147-148, indicate the threshold for differentially expressed genes using the DESeq2 program. Figure 1 is too small, so please display a simplified version indicating the number of genes in each group in the manuscript.
Thanks for giving me your suggestion. DESeq2 method (P＜0.05 and FoldChange＞＝2) was performed for detecting differential analysis of count data of different samples in M. domestica. We agree with this suggestion and have rearranged Figure 1, truncated the original figure, put I group on the left, and the II and III groups on the right.
6）The original Figure 1 can be moved to Supplementary Figure 1.
We apologize for this graph is completely illegible, have rearranged Figure 1.
7）Figure 2 can be reorganized, for example, by placing A on the upper panel and B, C, and D on the bottom panel.
Thanks for giving me your suggestion. We have tried to put B, C, and D below A, in fact B, C, and D is wider than A, there are white spaces on both sides of A, so the display is not as pretty as it used to be.
8）In Figure 4, please show one heatmap instead of two heatmaps in one column, and the legend of Figure 4 should describe the colors used in the heatmaps.
Thanks for giving me your suggestion. In Figure 4, A indicates the expression heatmap in different flowering development stages, B indicates the expression heatmap in different cultivars. So, we arranged two heatmaps in one column. Green color indicates that the expression levels of genes are low, while red color indicates that the levels are high.
9）In L300-327, it is important to describe how the authors obtained DEGs; if FPKM or TPM values were used in the heatmap, please provide details.
Thanks for giving me your suggestion. We added the threshold (P＜0.05 and FoldChange＞＝2) of DEGs screening in the method section, meanwhile, the data of heatmap is obtained from the FPKM value.
Reviewer 3 Report
In this study, the authors study the MIKCC-type MADS-box genes on Malus species using genome-wide analysis. The aims of this study are clear and the results are useful for future study. I don’t have strong negative comments but some minor suggestions that I put below:
1. The figure is hard to read and follow. In the current version, it is hard to read and catch the information from this phylogenetic tree. The authors need to think about how to present this figure in their manuscript.
2. For the MIKCC-type MADS-box genes in Malus species, domesticated apples and wild species, Malus baccata, have a different copy number of MIKCC-type MADS-box genes. The phylogenetic tree can link wild taxon and domesticated apples, but some of them cannot match (domesticated apples have, but wild taxon don’t find them, for example, the MD17G1065500, MD05G1037100, MD10G1041100, and MD17G1001300 find on domesticated apple, but cannot find on wild taxon.). The reason for this point is unclear.
3. The domesticated apple is of polyploid origin. It means the domesticated apple is polyploidy. It may be the reason that the copies of MIKCC-type MADS-box genes are higher in the domesticated apple. However, this manuscript does not focus on this point.
4. Could the authors draw the chromosomal locations of domesticated apples and wild taxon MIKC gene? I know it may be hard, but will be easy to figure out orthologous and paralogous regions.
5. For the identification and distribution of MIKCC-type MADS-box genes in 13 genome-released species, it may be not an important part of this manuscript.
Author Response
1. The figure is hard to read and follow. In the current version, it is hard to read and catch the information from this phylogenetic tree. The authors need to think about how to present this figure in their manuscript.
We apologize for the unclear graph, we have rearranged Figure 1, truncated the original figure, put I group on the left, and the II and III groups on the right.
2. For the MIKCC-type MADS-box genes in Malus species, domesticated apples and wild species, Malus baccata, have a different copy number of MIKCC-type MADS-box genes. The phylogenetic tree can link wild taxon and domesticated apples, but some of them cannot match (domesticated apples have, but wild taxon don’t find them, for example, the MD17G1065500, MD05G1037100, MD10G1041100, and MD17G1001300 find on domesticated apple, but cannot find on wild taxon.). The reason for this point is unclear.
We thank the reviewer for this comment. In the manuscript, we reported the present genes in the domesticated and wild apple genomes. We know clearly that the above four genes existed in domesticated apple but did not mention its orthologous genes in M. baccata. We are not sure if these genes absent in M. baccata genome for real or only were lacking due to the bad or incomplete assembly of M. baccata genome.
3. The domesticated apple is of polyploid origin. It means the domesticated apple is polyploidy. It may be the reason that the copies of MIKCC-type MADS-box genes are higher in the domesticated apple. However, this manuscript does not focus on this point.
We thank the reviewer for this comment. It’s true that the domesticated apple is of polyploid origin, but the domesticated apple is the diploid species, and experienced a recent whole genome duplication during the evolutionary history of apple reported by Velasco, R. et al.( Nat. Genet. 2010, 42, 833–839). To illustrate this issue, we added this description in the manuscript (Page 2, line 70-72).
4. Could the authors draw the chromosomal locations of domesticated apples and wild taxon MIKC gene? I know it may be hard, but will be easy to figure out orthologous and paralogous regions.
We thank the reviewer for this comment. Yes, it is hard to draw this figure to display the homologous relationship of MIKC genes between domesticated apple and wild taxon MIKC genes. Except that, the MIKC genes in the two genomes experienced tandem duplication events, and it’s a little hard to confirm the orthologous relationships. So in the manuscript we supplied the Table 2 to describe the relationship.
5. For the identification and distribution of MIKCC-type MADS-box genes in 13 genome-released species, it may be not an important part of this manuscript.
We thank the reviewer for this comment. We identified the MIKCC-type MADS-box genes in 13 genome-released species from the lower to higher organisms to trace the evolution of MIKCC-type MADS-box gene family. So this will help us to know the gene family comprehensively.
