Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts

Comments 1: In abstract, it is too long to read. Please re-write as concise as possible.

Response 1: Thank you for pointing this out. We have simplified it.

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Comments 2: Fig 1, please write full sentence rather than incomplete sentence and add more information based on conducting experiments. Increase resolution and enlarge all text and characters on Fig.  

Response 2: Agree. We have completed and enlarged the legend of Figure 1.

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Comments 3: Fig 2, do not need. Move to supplementary section.

Response 3: Thank you for pointing this out. We have placed it in Figure S5.

Comments 4: Fig 3, only use one figure and increase resolution.

Response 4: Thank you for pointing this out. We have removed the PCD 2D image and retained the PCD 3D image.

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Comments 5: Fig 4, add all information in legend.

Response 5: Thank you for pointing this out. The previous legend was relatively simple and has been added.

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Comments 6: Fig 5, I cannot interpret data. Please explain what do you want to say in this part.

Response 6: Thank you for pointing this out. We have made the following modifications: “The differential gene Venn diagram can clearly compare the differential genes of multiple combinations. The sum of all numbers in the circle represents the total number of differential genes in the comparison combination, and the overlapping area represents the common differential genes between combinations. The four pairs of comparison groups described above(EC338 vs EC333, EC338 vs W1767, EC338 vs P9060, EC333 vs H1522) were distinguished by a common differential gene of 2143, indicating that these genes were likely associated with resistance to eucalypt leaf blight.”

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Comments 7: Fig 6, based on the expression pattern that related with any genetic inheritance, you should add information of that explanation in discussion section how expression patterns correlated with genetic inheritance.   

Response 7: Thank you for pointing this out. We have added three references on the correlation between expression patterns and genetics in the discussion section.

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Comments 8: Fig 7-8, I cannot read anything. Please replace it. Add all information in legend.  

Response 8: Thank you for pointing this out.

We have enlarged Figure 6 and added the following legend: “(A: GO enrichment of EC338 vs EC333. B: GO enrichment of EC338 vs P9060. C: GO enrichment of EC338 vs W1767. D: GO enrichment of EC333 vs H1522.)”

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We have enlarged Figure 7 and added the following legend:”(A: KEGG enrichment of EC338 vs EC333. B: KEGG enrichment of EC338 vs P9060. C: KEGG enrichment of EC338 vs W1767. D: KEGG enrichment of EC333 vs H1522.)”

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Comments 9: Fig 11, I cannot read anything. Please replace it. Add all information in legend.

Response 9: Thank you for pointing this out. We have enlarged Figure 10 and added the following legend:”(A: Alternative Splicing event of EC338 vs EC333. B: Alternative Splicing event of EC338 VS P9060. C: Alternative Splicing event of EC338 VS W1767. D: Alternative Splicing event of EC333 VS H1522.)”

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Comments 10: In results, please describe as concise as possible to emphasize your logic and ideas. At this current version can not be focused.

Response 10: Thank you for pointing this out. We have Improved the results and added the 4. Conclusion section for a clear and concise summary, emphasizing the focus of the results section of this article.

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Comments 1: lines 110-111 “The percentage of susceptible area of the tested leaves was scanned using the software Leaf Doctor…” there is no reference to this software.

Response 1: Thank you for pointing this out. The reference of Leaf Doctor is same as the method of “spray inoculation”.

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Comments 2: lines 144-145 “In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality..” it should be poly(N) instead of ploy-N.

Response 2: Thank you very much to the reviewer for correcting the details. In our testing analysis method, poly -N was written, but according to the professional opinion of the reviewer, poly (N) has been replaced with poly -N.

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Comments 3: manuscript fragment lines 153 – 162 is rather unclear and should be rewritten

"And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene [27]. (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) performed using the DESeq2 R package (1.20.0) ...

Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor”.

Response 3: Thank you very much for the constructive suggestions provided by the reviewer regarding the methodology section. The original manuscript is too complex and repetitive here, and the expression is indeed not concise enough. It has been revised as follows: “And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene [27].

Differential expression analysis of two conditions was performed using the DESeq2 R package (1.20.0) (For DESeq2 with biological replicates) and the edgeR R package (3.22.5) (For edgeR without biological replicates). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. Unlike DESeq2, the read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Using absolute folding change 2 as the threshold for significant differential expression (Benjamini & Hochberg, P<=0.05) [28]. “

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4. Response to Comments on the Quality of English Language

Point 1: I am not qualified to assess the quality of English in this paper.

Response 1: Thank you very much for the reviewer's affirmation. I will double check and strive for excellence throughout the entire article.

5. Additional clarifications

Thank you again to the reviewer for their diligent reading and detailed suggestions, which have taken our manuscript to the next level.