Comparative Analysis of TPR Gene Family in Cucurbitaceae and Expression Profiling under Abiotic Stress in Cucumis melo L.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Specific comments:

The term "TPR genes" is repeated 103 times in the paper. Please double-check each and those that are not in italics.

Please review the text and clarify all abbreviations when they first appear in the paper

 

Line 15: Change Benincaceae to Benincaseae (put the word in italics)

Line 31: “are naturally exposed” change to “can be naturally exposed”

Line 64: Interacts, Its – please put lowercase letters there

Line 67: GA – put the full name in front of the abbreviation or explain somewhere what this abbreviation represents

Lines 129-130: put species names in italics

Line 158: add the word respectively to clarify the sentence

Lines 179-198: Why was it not stated how many TPR genes were isolated in the third group in both tribes?

Line 201: Change the sentence. It needs to be made clearer that it means 144 TPR proteins in cucurbit crops

Line 361 – 369: Explain why the number of TPR genes varies within the same species (between different cultivars)

Lines 77, 366, 367, 368, 374: Cucurbiteae instead of Cucubiteae

Lines 368 and 374: Benincaseae instead of Benicaseae

Line 368: Add clarification with the abbreviation WGD (Whole-genome duplication)

Line 395: Analysis with a lowercase letter

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

This article investigates the tetratricopeptide repeat (TPR) proteins, focusing on their evolution and function in Cucurbitaceae, a plant family that includes species like melon. The study identifies and characterizes 144 TPR genes from 11 genomes across eight Cucurbitaceae species, examining their distribution on chromosomes and evolutionary relationships. The research reveals that these genes play significant roles in melon development and response to various stresses.

Suggestions for Improving the Introduction:

The introduction could be more concise and focused. It should begin with a clear statement of the research's purpose and significance, specifically emphasizing the importance of studying TPR proteins in Cucurbitaceae.

Provide more context about the role of TPR proteins in other species before discussing their relevance in Cucurbitaceae. This will help readers understand the broader importance of the study.

Critical: Clearly state the main research questions or hypotheses that the study aims to address. This will give readers a clearer understanding of what the study is trying to achieve.

Critical: The botanical family name should not be italicized. When species names are presented for the first time, they must include the name of the author who described the species. For example: Cucumis melo L.

Suggestions for Improving the Methodology:

To enhance the manuscript's methodology section, it should offer more comprehensive explanations of the employed techniques and procedures. Specifically, the process of identifying and biochemically characterizing TPR genes warrants further elaboration. Additionally, incorporating a comparative analysis with other species would enrich the study. Detailing how the current methods diverge from or build upon prior TPR protein research can add valuable context and depth.

Greater focus on the visualization tools and techniques, such as the utilization of heatmaps for expression analysis, would aid in clarifying the interpretation of results. This approach will provide readers with a deeper understanding of the study's outcomes.

The reliance on certain databases, such as the Cucurbit Genome Database, and pre-existing genome characterizations might restrict the range of identified TPR proteins. Therefore, it is vital to more explicitly outline the criteria used for selecting these resources to ensure the study's reproducibility.

A thorough description of the bioinformatics tools used (like Blast, CDD, ExPASy, MEME, TBtools, MCScanX, PlantCARE, agriGo) and their specific settings (e.g., the e-value setting in Blast) is essential. This detailed account will facilitate replication and offer insight into the potential impact of these choices on the results.

The choice of the neighbor-joining method with MEGA-X for phylogenetic analysis is noted, yet the reasoning behind selecting this method over others is not elaborated upon. Enhancing the robustness of the phylogenetic tree could be achieved by employing multiple methods and comparing their outcomes.

The methodology and criteria used in software like Mapchat and TBtools for determining chromosomal locations and identifying duplication events need to be more comprehensively detailed, as these factors significantly influence result interpretation.

The article describes the process for identifying and analyzing cis-regulatory elements. However, it lacks detailed information on the statistical methods used for analysis and visualization in R language. Providing this information would enhance the accuracy and reliability assessment of the findings.

The employment of agriGo for Gene Ontology (GO) term analysis is mentioned, but the study falls short in explaining the selection of specific GO terms and the interpretation of P-values. These elements are pivotal for understanding gene functions.

The use of RNA-seq data and qRT-PCR for expression analysis is a critical aspect of the study. The manuscript should include comprehensive details on the experimental conditions, normalization methods in RNA-seq analysis, and validation of the qRT-PCR results. The reproducibility of expression analysis largely hinges on these aspects.

Given that the study focuses on the Cucurbitaceae family, it should incorporate a discussion on how the findings might be generalized or compared with other species or families.

For experimental reproducibility, it is crucial to clearly state the number of replicates, statistical analysis methods, and error measurement techniques used in the study.

 

Suggestions for Improving the Results and Discussion

The manuscript touches on whole-genome duplication (WGD) and its potential role in gene expansion. However, a more detailed discussion on how WGD and other evolutionary processes have influenced the diversity and function of TPR genes would be insightful.

The phylogenetic analysis is crucial, but the manuscript could benefit from a more detailed discussion of the implications of the phylogenetic relationships observed, especially regarding the evolutionary history and functional divergence of TPR genes.

The collinearity analysis and the construction of an integrated gene map are significant achievements. However, the manuscript could delve deeper into the evolutionary implications of these findings and discuss how they contribute to our understanding of genome organization and evolution in Cucurbitaceae.

The study provides an analysis of gene structure and motifs, but a more detailed discussion on how these structural elements contribute to the function and evolution of TPR genes would be beneficial.

The identification of cis-regulatory elements and GO terms is essential. However, the manuscript could further explore how these elements and terms relate to the biological functions and stress responses of TPR genes.

The expression analysis of CmTPR genes in various tissues and developmental stages is well-presented. Discussing how these expression patterns correlate with the physiological roles of these genes in plant development and stress responses would add depth.

The manuscript discusses the expression of CmTPR genes under various stress conditions. Expanding this section to discuss the potential mechanisms by which these genes contribute to stress tolerance would be valuable.

The discussion could benefit from a broader perspective on the implications of these findings for plant biology and agriculture, particularly in the context of Cucurbitaceae species. Additionally, outlining future research directions based on these findings would be beneficial.

Improving these aspects would significantly enhance the manuscript's contribution to the field, providing a more comprehensive understanding of TPR genes in Cucurbitaceae and their evolutionary and functional roles.

 

Comments on the Quality of English Language

Needs a small revision.

Author Response

Please see the attachment

Author Response File: Author Response.docx