Genome-Wide Characterization of the GRAS Gene Family in Cyclocarya paliurus and Its Involvement in Heterodichogamy
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsWang et al., present their findings related to the "Genome-Wide Characterization of the GRAS Gene Family in 2 Cyclocarya paliurus and Their Involvement in Heterodichogamy"
Overall, the manuscript writing is sound, and the methodology adopted is also fine. The results description and scientific discussion need improvement. The manuscript needs to be revised before accepted for publication. For details see comments below.
Earlier, the same research group published C. Paliurus genome. In this study, they identified the GRAS gene family.
There are a ton of published studies about the genome-wide identification and characterization of GRAS gene family in several different plant species. See some of those below. How is this study different from these other studies. In this study, (and most of the published papers) there is very less biological experimental data to backup the title claims.
1. Genome-Wide Characterization and Expression Profiling of the GRAS Gene Family in Salt and Alkali Stresses in Miscanthus sinensis (https://www.mdpi.com/1422-0067/23/23/14521)
2. Genome-wide identification and characterization of GRAS gene family in pigeonpea (Cajanus cajan (L.) Millspaugh) (https://link.springer.com/article/10.1007/s13205-023-03782-x)
It is not clear how Co-expression of CpRGL1 and CpGAI-2, and CpSCL6-2 implies their crucial roles in floral development and potential involvement in heterodichogamous flowering in C. paliurus.
I am also not satisfied with the science, its interpretation and critical discussion related to the role of GRAS genes/proteins in hetero-dichogamy.
Introduction Line 3. transcription factors.
Methodology. What is PA male flowers?
Why did the author restrict the length of GRAS proteins between 400-820 amino acids? This would significantly restrict/reduce the number of GRAS genes. Authros didnot find any GRAS gene on chr5, chr9 and chr15. Please discuss and compare with the other published papers I mentioned.
Heading 4.8. WGCNA not WGNCA
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsReview of the manuscript entitled: Genome-wide characterization of the GRAS gene family in Cyclocarya paliurus and their involvement in heterodichogamy submitted in MDPI Journal - Agronomy-3242535
The submitted manuscript uncovers expression profiles of the GRAS genes in the heterodichogamic flower buds of female and male of Cyclocarya paliurus. In this study the experimental purpose was to collect the flower buds at S3 developmental stage, for transcriptome analysis. However there is no information about the sequencing data and how the genes were extracted. I suggest, that author should wait until the sequence will be uploaded in database (in. eg. as Biological Project accession), before the manuscript publishing.
The main information is based on the available data in the internet and from the data previously published by Chen et al. 2019. Moreover there are many aspects underlined after bioinformatics analysis, which of course give the valuable evolutionary predictions, as well as the observation and conclusions are very interesting and well described.
The authors do not cite any references regarding the purpose of the selection of genes subjected to expression profiling and, as I understand, those indicated in the discussion were selected based on the heat map presented on Fig 7B.
The genes profiled by qRT-PCR tests may be considered as potential markers for monitoring the S3 stage of flower development in C. paliurus - t would indicate the application value of the conducted studies. However, I suggest adding a short paragraph devoted to qRT-PCR gene profiling. In addition, the CpSCL6 gene underlined in the discussion was not subjected to profiling; maybe it would be good to add its qRT-PCR profiles either.
Unfortunately, there is no access to all supplementation data. What does the attached excel table show? Is it the value of gene expression from sequencing? Do the values in the table provide comparisons of LogFC between stages S2, S3, S4 for protagyny and protandry flowers? For identified genes it could be good to present the Venn graph showing relationships between identified DEG’s (I suppose).
Taking into consideration of some suggestions the manuscript generally gives very interesting overview of the data analysis, and brings the new insights in the genetic regulation of the flowering mechanism of C. paliurus.
Regarding this suggestions and after upload the missing information the manuscript could be publish.
Comments on the Quality of English LanguageMinor editing required.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsThe authors investigated the molecular mechanisms of flowering genes in Cyclocarya paliurus and their involvement in heterodichogamy. Some comments.
It is necessary to provide the purpose of the study.
In the Materials and Methods section, highlight the statistical analysis subsection.
How do environmental conditions (stresses) affect GRAS genes in Cyclocarya paliurus and in which GRAS subfamilies, and does this affect heterodichogamy?
It is desirable to provide a microscopic analysis of male and female flowers at different stages of development.
It is desirable to provide an electron microscopic image of the localization of CpGRAS proteins in the nucleus, cytoplasm, and chloroplasts.
It is desirable to describe the molecular mechanism of interaction of CpGRAS proteins in the genetic network during the flowering period.
The list of references should be brought into line with the journal requirements.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
