Genome and Transcriptome Analysis of NF-Y Transcription Factors in Sweet Potato under Salt Stress
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsReviewers Comments
The article is well written and could be accepted after minor revisions. However, the plagiarism should be reduced below 20% and other comment are provided below.
Abstract
Comment 1: The title is comprehensive but consider simplifying it for better readability, "Genome and Transcriptome Analysis of NF-Y Transcription Factors in Sweet Potato Under Salt Stress".
Comment 2: Line 1-3: "Nuclear factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. This transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a crucial role in various biological processes in plants. Excellent introduction to NF-Y. Consider briefly mentioning the significance of this study in sweet potatoes upfront.
Comment 3: Line 4-6: "Despite its importance, the NF-Y gene family has not been reported in the sweet potato (Ipomoea batatas) genome. To address this gap, our research aimed to comprehensively catalogue and characterize the IbNF-Y genes in sweet potatoes." Clarify "IbNF-Y" when first mentioned, specifying it stands for sweet potato NF-Y genes.
Comment 4: Line 7-9: "Our study successfully uncovered 11 NF-YA, 21 NF-YB, and 5 NF-YC members within the species. We conducted an in-depth investigation into the IbNF-Ys, exploring their phylogeny, gene structure, chromosomal distribution, and conserved motifs." Consider specifying the total number of NF-Y genes identified in one statement for clarity.
Comment 5: Line 10-12: "Additionally, we examined expression patterns under salt stress conditions in both light and dark conditions by transcriptome sequencing, assessing specific NF-Y subfamily members' responses to these conditions." Rephrase to avoid redundancy, e.g., "Additionally, we assessed their expression patterns under salt stress in both light and dark conditions using transcriptome sequencing."
Comment 6: Line 13-15: "This thorough analysis not only lays the groundwork for future functional studies on individual NF-Y components but also elucidates their collective regulatory roles in stress responses." Consider highlighting one key finding or implication here for emphasis.
Introduction
Comment 6: Line 8-10: "The NF-Y complex plays a crucial role in facilitating complex assembly and nuclear translocation, processes that are essential for its DNA-binding mechanism." Consider breaking this sentence for readability, e.g., "The NF-Y complex facilitates complex assembly and nuclear translocation. These processes are essential for its DNA-binding mechanism."
Comment 7: Line 11-13 "Moreover, NF-Y subunits can form complexes with other transcription factors, thereby exerting regulatory control over the expression of downstream genes [3,4]." Good point. You might want to provide a specific example of such regulatory control.
Comment 8:- Line 14-15: "In plants, multiple genes encode each NF-Y subunit, resulting in numerous possible heterotrimeric combinations." Consider adding a sentence on the functional implications of these combinations.
Comment 9:- Line 16-18: "The unique organization of NF-Y subunits and their DNA-binding properties, along with the HFD’s ability to accommodate different protein modules, are plant-specific features that play a crucial role in development, growth, and reproduction [2]." This sentence is dense. Consider splitting it for better clarity.
Materials and Methods
Comment 10: Line 3-5: "Full-length protein alignments were performed using the MUSCLE software [59], and the resultant alignments were then imported into MEGA11 [30] to generate phylogenetic trees." Consider specifying the version of MUSCLE used.
Results
Comment 11:-Line 1-3: "To obtain the NF-Y gene family members in sweet potato, we utilized a hybrid approach combining BLASTP and HMM algorithms for analyzing the sweet potato genome. This approach resulted in the identification of 37 NF-Y family genes, consisting of 11 IbNF-YAs, 21 IbNF-YBs, and 5 IbNF-YCs." This is well-detailed. Ensure that the terms "BLASTP" and "HMM" are explained earlier for clarity.
Comment 12: Line 4-5: "Subsequently, we assigned names to these 37 IbNF-Y genes, ranging from IbNF-YA1 to IbNF-YA6, IbNF-YB1 to IbNF-YB12, and IbNF-YC1 to IbNF-YC5, respectively, based on their chromosomal locations and subfamilies." Consider explaining the naming convention in more detail.
Comment 13: Figure 3: The figure 3 could be replaced with a better dpi figure, as it is not very clear and difficult to read.
Comment 14: Figure 4: The figure could be separated into two figures, as in current form the figure A is not clearly visible.
Comments for author File: 
Comments.pdf
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsIn this work, the authors performed a comprehensive analysis including gene structure, conserved motifs, miRNA target site prediction, conserved region and structure analysis of NF-Y transcription factor in sweet potato. The authors identified 37 NF-Y members and further investigated their function in response to salt to clarify potential regulatory mechanisms of NF-Y in sweet potatoes.
Opinions:
1. Results showed that the authors identify 21 IbNF-YBs among a total of 37 NF-Y family genes, presenting in Table 1 and supplementary Table S1 (where I have highlighted by yellow-fill. However, I found that IbNF-YB12 and IbNF-YB13 are same by showing the same of gene sequence (CDS), amino acid sequence (protein); therefore, they also showed same pI and MW. Please clarify and re-analyze to confirm.
2. The figure data presented inside the manuscript file were low quality, Figure 3 and 4, especially. It might be caused during conversion or /paste options as picture, I guess. I recommend the author and/or journal production team should use the high-quality of original files which the author included in the supplementary.
3. As mentioned in the section 2.7, “Following salt treatment, samples were collected at 0-, 2-, 4-, 6-, and 8 hours under both light and dark conditions”. Could the authors explain in detail “light and dark conditions” mentioning there? Why were samples collected at dark conditions and what is purpose of collecting samples at these conditions?
Does that mean that apart from under long-day conditions (16-hour dark/8-hour light cycle) for sweet potato growing, the ʹHaida HD7791ʹsweet potato seedlings were exposed to an extra-light during the salt treatment, and then sampled for RNA-seq and designated as light conditions. Please describe detail for how the light and dark conditions were conducted.
4. Why did the authors include Rice for the synteny analysis of NF-Y genes (section 3.5)? I did not see this in the M&M.
5. About citation:
+ Please provide citation links of “hmmsearch program”, Pfam database, BLASTP search, ExPASy website (section 2.1), MEME-Suite online program (section 2.3), PlantCARE [65] database, ect... Cite style as the same way that the authors did for Conserved Domains Database (htps://www.ncbi.nlm.nih.gov/Structure) or psRNATarget website (htps://www.zhao-lab.org/psRNATarget/analysis?function=3. Since these citations #56,57,58 are references which showed and given guidance for how do analysis and generate based on browsing/online software. Therefore, these citations should be presented and provided with access links.
+ The citation #61 (TBtools) should be cited once the first time it was mentioned, while it was cited 4 times for sections 2.3 and 2.4.
6. The authors should provide the Accession number/GeneBank in the Supplementary Table S5.
Minor remarks:
- (Table 1): Italicize “I. batatas” and table footnote (“pI: isoelectric points, MW: Molecular Weight”) should be removed since these abbreviations have already been presented in full form in the body of section 3.1.
- “Subunits” (Section 3.2) should be replaced by “subfamilies”.
- Italicize genes: PdNCED, IbNF-YB21, NF-Y (Section 4.3)
It is a little difficult for me to point out the place-in-text that needs to be attention since the manuscript did not include the line number. Therefore, I have marked the above comments and others directly on the manuscript in the blue-marked and comment box. Please check and revise.
Comments for author File: Comments.zip
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Comments and Suggestions for AuthorsA manuscript by Liang et al. has identified and characterized 37 putative NF-Ys (11 NF-YA, 21 NF-YB, and 5 NF-YC), and examined their expression patterns. However, they provided only preliminary data (obtained by simple-database-mining), which is insufficient to conclude that these putative genes are 'true NF-Y'. At least, complementation analysis using Arabidopsis T-DNA mutants is needed.
Author Response
Comment: A manuscript by Liang et al. has identified and characterized 37 putative NF-Ys (11 NF-YA, 21 NF-YB, and 5 NF-YC), and examined their expression patterns. However, they provided only preliminary data (obtained by simple-database-mining), which is insufficient to conclude that these putative genes are 'true NF-Y'. At least, complementation analysis using Arabidopsis T-DNA mutants is needed.
Response: Thank you for your thoughtful review and valuable comments on our manuscript. We appreciate your suggestion regarding the functional validation of the identified NF-Y genes. However, we regret to inform you that conducting complementation analysis using Arabidopsis T-DNA mutants is beyond the current scope and resources of our study.
Our primary aim was to identify and characterize the NF-Y gene family in sweet potato through comprehensive bioinformatics analyses. We have thoroughly examined their expression patterns and provided detailed insights into their potential roles. While we understand the importance of functional validation, the preliminary data we presented offer a solid foundation for future experimental studies.
We believe that our findings significantly contribute to the existing knowledge of the NF-Y gene family in sweet potato and lay the groundwork for more in-depth functional studies. We hope that the current data will be valuable to the research community and inspire further experimental validation studies.
