Interspecies Conservation of Gene Expression Patterns in Brassica Reproductive Organs Unveiled by Comparative Transcriptomics

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Summary

Manuscript is quite interesting, and the analysis of dataset was successfully done. The manuscript lacks line numbers. Additionally, the Introduction section should be reinforced to provide a more comprehensive background. Discussion should interpret the biological implications behind the differential gene expression observed across various organs, linking them to the distinct plant architectures of the Brassica species within the U’s triangle.

Abstract

The species within the U’s triangle should be explicitly mentioned. Additionally, the specific organs analyzed must be clearly stated. It is also important to specify that the data were retrieved from a database.

Introduction

The importance of whole transcriptome sequencing in investigating differential genetic patterns within the Brassica genus should be further emphasized. This is crucial for ensuring high productivity standards under multiple stress conditions and for understanding the genetic architecture of flowering processes. Additionally, a comparison between de novo and reference-based transcriptomic approaches should be highlighted.

To strengthen this section, I highly recommend incorporating the following references: https://doi.org/10.1016/j.stress.2024.100657; https://doi.org/10.3389/fgene.2022.958217; https://doi.org/10.1016/j.gene.2013.12.057

Additionally, the paragraph introducing the aim of the study should be more concise and to the point.

Results

Figure descriptions must be more detailed, explicitly specifying the software used to generate each plot.

In Figure 3, the meaning of the different colors used should be clearly explained.

Discussion

The Discussion should interpret the biological implications behind the differential gene expression observed across various organs, linking them to the distinct plant architectures of the Brassica species within the U’s triangle.

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The presented article is devoted to the comparison of different genes’ expression patterns during growth and development of relative Brassica species on the basis of published data. Authors formed an atlas of different gens’ expression patterns and compared the expression of similar genes in relative species.

At the same time, there is no information (and discussion) about environmental conditions in which evaluated genes were expressed. It is no use to compare genes’ expression if plants were grown in different conditions. Even if plants were grown in equal conditions, they must be discussed, because they straightly influence genes’ expression.

Also, there is no conclusion in the article.

Article contains a lot of untraditional and unevident abbreviations. It will be better to include the list of abbreviations. Another solution is not to use them, because the volume of the article is not limited.

Figures are too small. It is practically impossible to digest them if printed.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Dear Authors,

Reviewer comments horticulturae-3535882

The manuscript entitled „Interspecies conservation of gene expression patterns in Brassica reproductive organs unveiled by comparative transcriptomics“ represents a useful study aimed at a comparison of gene structure, phylogenetic analysis, and expression patterns of YABBY and GRF transcription factors in major Brassica crop species including Brassica rapa (AA), Brassica nigra (BB), Brassica oleracea (CC), Brassica juncea (AABB), Brassica napus (AACC), and Brassica carinata (BBCC). The manuscript provides complex data on YABBY and GRF transcription factor families in economically important Brassica species. I can recommend the manuscript publication in Horticulturae.

I have only some comments on Figure 7 and Figure 8 providing phylogenetic trees of YABBY and GRF transcription factors in Brassica species: In both figure legends, information on the algorithm and the software used for the phylogenetic tree construction has to be added.  Moreover, appropriate statistics has to be added directly to both phylogenetic trees which are just schemes without statistical treatment. I should recommend the authors to add bootstrap values indicating the probability of branching per 1,000 replicates at each node.

In the text right above Figure 7, add the words „YABBY genes“ in the statement: „…we found that the dominantly expressed in YABBY genes in the embryo were YABBY1 and YABBy5 (Table S10).“

 

Final recommendation: Accept after a minor revision.

 

Comments for author File: Comments.pdf

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Authors addressed all the reviewer's comments

Reviewer 2 Report

Comments and Suggestions for Authors

The article was improved and now it can be published