Transcriptome Analysis of Embryogenic and Non-Embryogenic Callus of Picea Mongolica
Round 1
Reviewer 1 Report
In the article “Transcriptome Analysis of Embryogenic and Non-Embryogenic Callus of Picea mongolica”, the author are comparing the embryogenic callus (EC) and non-embryonic callus (NEC) of Picea mongolica, a rare tree species in China. The study aims to understand the differences between EC and NEC at the morphological, histological, physiological, and transcriptional levels. The findings of the study have implications for the micro-proliferation of P. mongolica, which is important for combating desertification and improving the ecological environment.
The manuscript is well-written, I only have a few minor suggestions, listed below.
- Keywords should be arranged alphabetically. Moreover, please, do not repeat words from the title.
- Please, provide the initials of the author of the species’ name when mentioning it for the first time, e.g. in the Abstract.
- Throughout the text, authors are mixing common and scientific names of species.
- All abbreviations must be explained when first mentioned, regardless of the Abstract.
- Line 90: what does mean “normal medium”?
- Line 95: “media” or “cultures”?
- More details of the producers of key chemicals and equipment is need, i.e. the name, city, state and country.
- Figures lack scale bars.
- Avoid repetitions, e.g. in the Introduction and Discussion.
- References lack DOI numbers.
- The English style is generally good, although minor punctuation correction is needed.
After making all the necessary changes, the article can be accepted for publication.
The English style is generally good, although minor punctuation correction is needed.
Author Response
Reviewer 1
In the article “Transcriptome Analysis of Embryogenic and Non-Embryogenic Callus of Picea mongolica”, the author are comparing the embryogenic callus (EC) and non-embryonic callus (NEC) of Picea mongolica, a rare tree species in China. The study aims to understand the differences between EC and NEC at the morphological, histological, physiological, and transcriptional levels. The findings of the study have implications for the micro-proliferation of P. mongolica, which is important for combating desertification and improving the ecological environment.
Author response:
Thank you so much for consideration of our manuscript and giving a positive response. We appreciate the opportunity to revise and further improve our manuscript. We have made some major modifications to the revised version of the manuscript. We hope you will find it better now.
- Keywords should be arranged alphabetically. Moreover, please, do not repeat words from the title.
Author response:
Dear Reviewer, we have replaced the keywords as suggested by you and arranged them alphabetically.
- Please, provide the initials of the author of the species’ name when mentioning it for the first time, e.g. in the Abstract.
Author response:
As suggested by the reviewer, we have changed the species names as "Picea mongolica" in the Abstract and "Picea morrisonicola", "Picea koraiensis", "Picea likiangensis", "Picea abies", and "Picea rubens" in Introduction.
- Throughout the text, authors are mixing common and scientific names of species.
Author response:
Thank you for pointing this out. We have changed "Norway Picea”, "Cotton" and "banana" to the scientific names "Picea abies", "Gossypium hirsutum L." and "Musa spp.", respectively.
- All abbreviations must be explained when first mentioned, regardless of the Abstract.
Author response: As suggested by the respected reviewer, we have provided explanations for all initial abbreviations in the paper, e.g. "embryogenic callus (EC)”, "non-embryonic callus (NEC)", "somatic embryogenesis (SE)”, “polyethylene glycol (PEG)" and "transcription factors (TFs) ".
- Line 90: what does mean “normal medium”?
Author response: Thank you for pointing this out. We have replaced "normal medium" with "proliferation medium".
- Line 95: “media” or “cultures”?
Author response: We have changed “media” to “cultures” or “culture”.
- More details of the producers of key chemicals and equipment are needed, i.e., the name, city, state and country.
Author response: As per reviewer suggestion, we have provided a source description of the key chemicals and equipment involved in the paper, e.g., "(Agilent, CA, USA)”, "(NEB, MA, USA)", "(Bio-Rad, CA, USA)" and "(Vazyme, Nanjing, China)".
- Figures lack scale bars.
Author response: Dear reviewer, we have modified the scale bars in Figure 1 and Figure 2 for a clearer view. In addition, appropriate scales have been added to Figures 8.
- Avoid repetitions, e.g., in the Introduction and Discussion.
Author response: Thank you for pointing this out. We have revised the Introduction and Discussion section to avoid repetition and make them more attractive in the updated manuscript file for better understanding.
- References lack DOI numbers.
Author response: As suggested by the reviewer, we have added the available DOI numbers to the reference list.
Reviewer 2 Report
In the manuscript entitled “Transcriptome Analysis of Embryogenic and Non-Embryogenic
Callus of Picea mongolica”, the authors showed the changes that occur in the gene expression profile, morphology, histology, and physiology during the differentiation of Picea mongolica non-embryonic callus (NEC) to embryonic callus (EC). Picea mongolica is a rare tree with tolerance to sand-burying, drought, and cold. It is also an economically important tree used in manufacturing furniture, musical instruments, and paper. However, Picea mongolica is susceptible to pests, high mortality, and a low rate of natural regeneration. Breeding and somatic embryogenesis (SE) are the current methods of increasing Picea mongolica cultivation. The authors previously established a regeneration system for Picea mongolica by SE, but discovered that induction efficiency from NEC to EC was low and took a long time. Therefore, to shorten the induction time from NEC to EC and to increase the rate of EC induction, the authors want to determine the genes involved in the process, along with the molecular mechanism.
In this study, the authors examined the morphology, cytology, and physiology of Picea mongolica NEC and EC, and analyzed their gene expression using RNA-seq. In terms of morphology, their studies showed that EC is white and transparent filamentous, while NEC is lumpy, compact, and brownish. Histological studies indicate that NEC cells are large and loosely arranged, while EC cells are small and closely arranged. Physiological determinations showed that the activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and polyphenol oxidase (PPO) were much higher in EC than NEC, but the activity of peroxidase (POD) in NEC was more than EC. Transcriptome analysis revealed 3682 up-regulated genes and 9585 down-regulated genes. These differentially expressed genes were divided into the different biological processes that regulate SE. The processes include hormone signaling, stress signaling, phenylpropanoid signaling, and transcription factors. In sum, this study provides a solid foundation for identifying crucial genes that are important for shortening the induction time from NEC to EC and increasing the rate of EC induction, which will increase Picea mongolica cultivation.
Is the manuscript clear, relevant for the field and presented in a well-structured manner?
Yes, the manuscript is clear, relevant for the field and presented in a well-structured manner.
Are the cited references mostly recent publications (within the last 5 years) and relevant? Does it include an excessive number of self-citations?
Yes, the references are recent and relevant, without excessive self-citations.
Is the manuscript scientifically sound and is the experimental design appropriate to test the hypothesis?
Yes, the manuscript is scientifically sound, and the experimental design is appropriate to test the hypothesis.
Are the manuscript’s results reproducible based on the details given in the methods section?
Yes, the methods are detailed and can be easily followed to repeat the results presented.
Are the figures/tables/images/schemes appropriate? Do they properly show the data? Are they easy to interpret and understand? Is the data interpreted appropriately and consistently throughout the manuscript?
Yes, all of the figures are appropriate, simple to follow, and to understand. However, for figure 3, it is difficult to see and read the labels.
Are the conclusions consistent with the evidence and arguments presented?
Yes, the results support the conclusions drawn.
1. What is the main question addressed by the research?
The authors previously established a regeneration system for Picea mongolica by SE. However, they discovered that induction efficiency from NEC to EC was low and took a long time. Therefore, to shorten the induction time from NEC to EC and to increase the rate of EC induction, the authors want to determine the genes involved in the process, along with the molecular mechanism.
2. Do you consider the topic original or relevant in the field?
This study is relevant to the field because it provides the transcriptomic profile for Picea mongolica NEC and EC which reveals differentially expressed genes. It shows genes for hormone signaling, stress signaling, phenylpropanoid signaling, and transcription factors that are important SE, which can be explored to increase the rate of NEC induction to EC. This study also provides important insights into the morphology, cytology, and physiology of Picea mongolica NEC and EC.
Does it address a specific gap in the field?
The authors used RNA-Seq to perform a comparative transcriptome analysis of Picea mongolica NEC and EC. Their analysis provides new insight into gene profiles between NEC and EC which helps to better understand SE in Picea mongolica.
3. What does it add to the subject area compared with other published material?
This study provides a solid foundation for identifying crucial genes that are important for shortening the induction time from NEC to EC and increasing the rate of EC induction, which will increase Picea mongolica cultivation.
4. What specific improvements should the authors consider regarding the methodology? What further controls should be considered?
The methodology is straightforward and nothing significant is lacking to replicate the analyses and experiments.
No additional controls are needed for the scope of this study.
5. Are the conclusions consistent with the evidence and arguments presented and do they address the main question posed?
Yes, the conclusions are consistent with the results provided. All of the data presented are relevant to the main question the authors are addressing.
6. Are the references appropriate?
Yes, the references are appropriately relevant to the study.
7. Please include any additional comments on the tables and figures.
* In figure 3, it is difficult to see and read the labels. The authors should consider revising this figure.
· There are some typing mistakes, especially in the discussion section that should be fixed.
There are no issues with quality of English, but there are some typing mistakes that should be fixed.
Author Response
Reviewer 2
This study provides a solid foundation for identifying crucial genes that are important for shortening the induction time from NEC to EC and increasing the rate of EC induction, which will increase Picea mongolica cultivation.
Author response:
Thank you so much for consideration of our manuscript and giving a positive response. We appreciate the opportunity to revise and further improve our manuscript. We have made modifications to the revised version of the manuscript. We hope you will find it better now.
- In figure 3, it is difficult to see and read the labels. The authors should consider revising this figure.
Author response:
Dear Reviewer, we have replaced figure 3 with a clearer picture for better reading as suggested by you.
- There are some typing mistakes, especially in the discussion section,that should be fixed.
Author response:
Thank you for pointing this out. We have corrected all typos and grammatical mistakes.
