Transcriptomic Analysis of Medicago truncatula under Long-Day Conditions
Round 1
Reviewer 1 Report
Journal Diversity (ISSN: 1424-2818)
Manuscript ID: diversity-2548642
Type of manuscript: Article
Title: Transcriptomic analysis of Tribulus terrestris alfalfa under long day
conditions
Authors: Luo Wen Ju, Li Yajiao, Lu Xue Ping, Tong Wei Yang, Caijun Chen, Ma
Peijie, Zehui Chen *, Xiaoli Wang *
Submitted to section: Plant Diversity,
Abstract
To explore the expression characteristics and biological functions of genes of Medicago truncatula under long day conditions, and to lay a foundation for revealing the molecular mechanism of Medicago truncatula under long day conditions.
Replace
The objective of this research was to understand the expression characteristics and biological functions of Medicago truncatula genes under long day conditions.
Abstract
The leaves of 'R108' tribulus Medicago sativa at branch stage (A), bud stage (B), initial flowering stage (C) and full flowering stage (D) were sequenced by RNA-Seq technology.
Replace
The leaves of 'R108' tribulus Medicago trucatula at branch stage...
Abstract
The transcriptomes of three adjacent periods (A vs B, B vs C, C vs D) were analyzed for differentially expressed genes and photoperiod related differentially expressed genes were screened.
Replace
The transcriptomes of three adjacent periods (A vs B, B vs C, C vs D) were analyzed for differentially gene expression and these genes were screened.
Abstract
...among which the most differentially expressed genes were involved in cell components.
Replace
...among which the most differentially expressed genes were involved in the synthesis of cell componentes .
Abstract
...were thehighest. The function of eggNOG was divided into 23 categories, with a total of 26745 genes havingsimilarities, 9008 genes were classified as function unknown, 2669 genes were classified as signaltransduction mechanism, 2194 genes were classified as transcription, etc.
Replace
What etc means??
Abstract
The difference between up-regulated and down-regulated genes was the most obvious between bud stage and initial flowering stage.
Replace
The difference between up-regulated and down-regulated genes was more noteworthy among the bud stage and the initial flowering stage.
Keywords replace
Photoperiod, gene expression, transcriptome analysis, molecular mechanism
Introduction
Currently, most studies on photoperiodic regulation of flowering have focused on the model plant Arabidopsis thaliana, and have a comprehensive understanding of the involved
Replace
Currently, most studies on photoperiodic regulation of flowering have focused on the model plant Arabidopsis thaliana, providing a comprehensive understanding of the involved....
Introduction
Therefore, it is importante to understand the mechanisms of flowering regulation in the model plant Arabidopsis thaliana for the regulation of flowering in thistles and clover.
Explain
in the model plant Arabidopsis thaliana for the regulation of flowering in thistles and clover. What this means?
Introduction
Medicago truncatula, belonging to the legume family, is an annual forage plant with madvantages
Replace
...advantages
Introduction
self-pollination, high fruiting rate, etc.
Explain
Etc..???? . What this means?
Introduction
bases for the study of legume forage grasses and genomics
Explain
legume forage grasses
Material and methods
...on 13 February, 28 February, 27 March and 17 April 2023 separately. Four different periods of Medicago truncatula leaf samples were labelled as meristematic stage (A), bud stage (B), first flowering stage (C) and full flowering stage (D) respectively.
Replace
...on 13 February, 28 February, 27 March and 17 April 2023 separately, representing the meristematic stage (A), bud stage (B), first flowering stage (C) and full flowering stage (D) respectively.
Results
3.1. Analysis of RNA-seq sequence
In order to further resolve the key genes affected in the molecular regulatory network pathways of Medicago truncatula at different developmental stages, the differentially expressed genes between different developmental stages of Medicago truncatula were analysed by using transcriptome sequencing technology (RNA-seq). The above Medicagotruncatula was planted under long sunlight conditions, and leaf samples were taken at the branching stage (A), the bud stage (B), the first flowering stage (C) and the full flowering stage (D) for transcriptome sequencing analysis. After sequencing quality control, the number of reads in the raw data of each sample group
Replace
This is Matherial and methods: remove
Results
3.3. Domporisom of differentials expressed genes
The differentially expressed genes between adjacent time periods (A vs B, B vs C, C vs D)...
Replace
The differentially expressed genes among developmental stages (A vs B, B vs C, C vs D)...
Conclusion
Gene expression profiling data were obtained from leaves of 'R108' Medicago truncatula at four growth and development periods, and 51 differentially expressed genes were involved in the photoperiodic pathway, including 23 up-regulated genes and 28 down-regulated genes. These genes may be involved in the regulation of flowering synthesis in Medicago truncatula.
Very poor statemnet. It is just a description of the results. It needs to explore the possible use of this informationfor the researches that could use this data. What are the consequences for plant breeding for example? And so on
General observations
Although the data obtained in this work was valuable and was obtained using the wright methods the general texto f the manuscript needs to be revised and rewrighted. The text also needs to explore better how this information could be used to researchers working with this species and othres forage legumes using Medicago trunculata as a plant model.
Comments for author File: 
Comments.pdf
Author Response
review-1：
Journal Diversity (ISSN: 1424-2818)
Manuscript ID: diversity-2548642
Type of manuscript: Article
Title: Transcriptomic analysis of Tribulus terrestris alfalfa under long day
conditions
Authors: Luo Wen Ju, Li Yajiao, Lu Xue Ping, Tong Wei Yang, Caijun
Chen, Ma
Peijie, Zehui Chen *, Xiaoli Wang *
Submitted to section: Plant Diversity,
Abstract
To explore the expression characteristics and biological functions of genes of Medicago truncatula under long day conditions, and to lay a foundation for revealing the molecular mechanism of Medicago truncatula under long day conditions.
Replace
The objective of this research was to understand the expression characteristics and biological functions of Medicago truncatula genes under long day conditions.
Teacher, you have worked hard, has been carefully modified, please check
Abstract
The leaves of 'R108' tribulus Medicago sativa at branch stage (A), bud stage(B), initial flowering stage (C) and full flowering stage (D) were sequenced by RNA-Seq technology.
Replace
The leaves of 'R108' tribulus Medicago trucatula at branch stage...
Teacher, you have worked hard, has been carefully modified, please check
Abstract
The transcriptomes of three adjacent periods (A vs B, B vs C, C vs D) were analyzed for differentially expressed genes and photoperiod related differentially expressed genes were screened.
Replace
The transcriptomes of three adjacent periods (A vs B, B vs C, C vs D) were analyzed for differentially gene expression and these genes were screened.
Teacher, you have worked hard, has been carefully modified, please check
Abstract
...among which the most differentially expressed genes were involved in cell components.
Replace
...among which the most differentially expressed genes were involved in the synthesis of cell componentes.
Teacher, you have worked hard, has been carefully modified, please check
Abstract
...were thehighest. The function of eggNOG was divided into 23 categories, with a total of 26745 genes havingsimilarities, 9008 genes were classified as function unknown, 2669 genes were classified as signaltransduction mechanism, 2194 genes were classified as transcription, etc.
Replace
What etc means??
Teacher, you have worked hard, has been carefully modified, please check
Abstract
The difference between up-regulated and down-regulated genes was the most obvious between bud stage and initial flowering stage.
Replace
The difference between up-regulated and down-regulated genes was more noteworthy among the bud stage and the initial flowering stage.
Teacher, you have worked hard, has been carefully modified, please check
Keywords replace
Photoperiod, gene expression, transcriptome analysis, molecular mechanism
Teacher, you have worked hard, has been carefully modified, please check
Introduction
Currently, most studies on photoperiodic regulation of flowering have focused on the model plant Arabidopsis thaliana, and have a comprehensive understanding of the involved
Replace
Currently, most studies on photoperiodic regulation of flowering have focused on the model plant Arabidopsis thaliana, providing a comprehensive understanding of the involved....
Teacher, you have worked hard, has been carefully modified, please check
Introduction
Therefore, it is importante to understand the mechanisms of flowering regulation in the model plant Arabidopsis thaliana for the regulation of flowering in thistles and clover.
Explain
in the model plant Arabidopsis thaliana for the regulation of flowering in thistles and clover. What this means?
Sorry for the mistake, it is not in thistles and clover, it is Medicago truncatula, because Arabidopsis Thistles, as a model plant, has a certain representative, using it for comparison, the study of Tribulus thistles alfalfa is of high value.
Introduction
Medicago truncatula, belonging to the legume family, is an annual forage plant with madvantages.
Replace
...advantages
Teacher, you have worked hard, has been carefully modified, please check
Introduction
self-pollination, high fruiting rate, etc.
Explain
Etc..???? . What this means?
Teacher, you have worked hard, has been carefully modified, please check
Introduction
bases for the study of legume forage grasses and genomics
Explain
legume forage grasses
It has been revised and relevant literature has been added
Material and methods
...on 13 February, 28 February, 27 March and 17 April 2023 separately. Four different periods of Medicago truncatula leaf samples were labelled as meristematic stage (A), bud stage (B), first flowering stage (C) and full flowering stage (D) respectively.
Replace
...on 13 February, 28 February, 27 March and 17 April 2023 separately, representing the meristematic stage (A), bud stage (B), first flowering stage (C) and full flowering stage (D) respectively.
Teacher, you have worked hard, has been carefully modified, please check
Results
3.1. Analysis of RNA-seq sequence
In order to further resolve the key genes affected in the molecular regulatory network pathways of Medicago truncatula at different developmental stages, the differentially expressed genes between different developmental stages of Medicago truncatula were analysed by using transcriptome sequencing technology (RNA-seq). The above Medicagotruncatula was planted under long sunlight conditions, and leaf samples were taken at the branching stage (A), the bud stage (B), the first flowering stage (C) and the full flowering stage (D) for transcriptome sequencing analysis. After sequencing quality control, the number of reads in the raw data of each sample group
Replace
This is Matherial and methods: remove
Teacher, you have worked hard, has been carefully modified, please check
Results
3.3. Domporisom of differentials expressed genes
The differentially expressed genes between adjacent time periods (A vs B, B vs C, C vs D)...
Replace
The differentially expressed genes among developmental stages (A vs B, B vsC, C vs D)...
Teacher, you have worked hard, has been carefully modified, please check
Conclusion
Gene expression profiling data were obtained from leaves of 'R108' Medicago truncatula at four growth and development periods, and 51 differentially expressed genes were involved in the photoperiodic pathway, including 23 up-regulated genes and 28 down-regulated genes. These genes may be involved in the regulation of flowering synthesis in Medicago truncatula.
Very poor statemnet. It is just a description of the results. It needs to explore the possible use of this informationfor the researches that could use this data. What are the consequences for plant breeding for example? And so on
Has been carefully revised, reflected in the article. Thank you, teacher, the most sincere greetings.
General observations
Although the data obtained in this work was valuable and was obtained using the wright methods the general texto f the manuscript needs to be revised and rewrighted. The text also needs to explore better how this information could be used to researchers working with this species and othres forage legumes using Medicago trunculata as a plant model.
It has been carefully modified, please check the teacher, there is a wrong place, please ask the teacher to propose, we further carefully modified, thank you, teacher, you have worked hard!
Dear teacher, hello, according to your requirements, we have been very serious in the revision, the revised content is reflected in the revised draft, some modifications have no traces, but all have been modified, please check, thank you, I wish the teacher happy every day, family happiness, career is getting better and better.
Author Response File: 
Author Response.docx
Reviewer 2 Report
The manuscript requires a sentence structure check as well as extensive editing. The sentences are too long for the reader's attention.
Arabidopsis thaliana should be in italics and after first usage should be typed as A. thaliana. Please italicize the scientific names of all plants mentioned in the text.
All gene names should be italicised.
At Co should be italics, please expand CO.
The second sentence of the introduction is too long. Consider revising.
The space between gene name and number should be deleted, for eg. phy A should be typed as phyA
The response regulator (PRR) family - expand PRR
"Therefore, it is important to understand the mechanisms of flowering regulation in the model plant Arabidopsis thaliana for
the regulation of flowering in thistles and clover." This sentence gives the idea that the authors will be using A. thaliana in this study. Please rephrase.
"The samples were quick-frozen in liquid nitrogen, embedded"I believe the samples were stored in dry ice for transportation and not embedded.
More details are needed on the RNA isolation procedure (if Trizol or kit was used), how was the quality (260/280 and RIN number), which kit was employed for cDNA synthesis
Cite the link for reference genome
The legends should be more informative and should have what A, B, C, and D samples are!
Why did the authors not compare A vs. C, B vs. D, and A vs. D?
Inconsistency in the fonts of figure numbering
The manuscript requires extensive editing.
Author Response
review-2：
The manuscript requires a sentence structure check as well as extensive editing. The sentences are too long for the reader's attention.
Teacher, you have worked hard, has been carefully modified, please check
Arabidopsis thaliana should be in italics and after first usage should be typed as A. thaliana. Please italicize the scientific names of all plants mentioned in the text. Arabidopsis thaliana.
Teacher, you have worked hard, has been carefully modified, please check
All gene names should be italicised.
Teacher, you have worked hard, has been carefully modified, please check
At Co should be italics, please expand CO.
Teacher, you have worked hard, has been carefully modified, please check
The second sentence of the introduction is too long. Consider revising.
Teacher, you have worked hard, has been carefully modified, please check
The space between gene name and number should be deleted, for eg. phy A should be typed as phyA
Teacher, you have worked hard, has been carefully modified, please check
The response regulator (PRR) family - expand PRR
Teacher, you have worked hard, has been carefully modified, please check
"Therefore, it is important to understand the mechanisms of flowering regulation in the model plant Arabidopsis thaliana for the regulation of flowering in thistles and clover." This sentence gives the idea that the authors will be using A. thaliana in this study. Please rephrase.
Teacher, you have worked hard, has been carefully modified, please check
"The samples were quick-frozen in liquid nitrogen, embedded" I believe the samples were stored in dry ice for transportation and not embedded.
Teacher, you have worked hard, has been carefully modified, please check
More details are needed on the RNA isolation procedure (if Trizol or kit was used), how was the quality (260/280 and RIN number), which kit was employed for cDNA synthesis
Teacher, you have worked hard, has been carefully modified, please check
Cite the link for reference genome
Teacher, you have worked hard, has been carefully modified, please check
The legends should be more informative and should have what A, B, C, and D samples are!
Teacher, you have worked hard, has been carefully modified, please check
Why did the authors not compare A vs. C, B vs. D, and A vs. D?
Dear teacher, our research is the adjacent growth and development stage, and we have seen many papers, which also study the adjacent stages, but A and C, B and D, A and D are equally important, and they are also the places we have neglected. In the following research, the development stage of non-adjacent stages will be the focus of our research.
Inconsistency in the fonts of figure numbering
Teacher, you have worked hard, has been carefully modified, please check
Dear teacher, hello, according to your requirements, we have been very serious in the revision, the revised content is reflected in the revised draft, some modifications have no traces, but all have been modified, please check, thank you, I wish the teacher happy every day, family happiness, career is getting better and better.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
The conclusion must be improved. it remain as just a description of the results. It needs to explore the possible use of this informationfor the researches that could use this data. What are the consequences for plant breeding for example? And so on
Author Response
Dear teacher, hello, we have carefully revised the conclusion, please check it. The teacher you have worked hard, I wish the teacher happy every day, the family is happy and everything goes well.
Based on RNA-Seq technology, this study revealed the transcriptomic map of different developmental stages of Medicago truncatula under long day conditions and found that there were significant gene differences in different developmental stages of Medicago truncatula under long day conditions. 6875 differentially expressed genes, comprising 3463 up-regulated genes and 3412 down-regulated genes, were found by comparing the gene expression of leaves at various developmental stages. As a consequence of functional annotation and enrichment analysis, it was shown that the differentially expressed genes were primarily connected to pathways for ribosome metabolism, photosynthesis-related proteins, and circadian rhythms. The reaction to prolonged long day conditions was also discovered to be regulated by 51 photoperiod-related differentially expressed genes at various stages of Medicago truncatula development. These results provided a theoretical basis for transcriptomic studies on the leaves of Medicago truncatula in different developmental stages, and provided new insights for plant breeding. Finally, they laid a foundation for the exploration of the function of the differentially expressed genes in the late stage of Medicago truncatula and provided basic sequences for the study of flowering regulation mechanisms and flowering-related genes, which had important significance for the subsequent study of adaptability breeding of leguminous forage.
