Genome-Wide Identification and Expression Analysis Reveal bZIP Transcription Factors Mediated Hormones That Functions during Early Somatic Embryogenesis in Dimocarpus longan

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In this study, bZIP family members in longan were systematically identified and a comprehensive bioinformatics analysis of DlbZIP (bZIP family members) was performed, and subcellular localization and profiles patterns after transiently transformed DlbZIP60 were analyzed. The study found that DlbZIP family were closely related to dicotyledonous plants.

The author should have a Figure of somatic embryogenesis process

Line 199, Starting from 2.5, and the paragraphs should be aligned left and right;

Notice to the spaces and some spellings; such as line 13; line 244;

Some need abbreviation, e.g. μM instead of μmol^-1;

Some Latin names need to be italicized, such as Agrobacterium tumefaciens; Some English botanical names require a Latin names; such as Line176, 369-372;

Some grammar requires the past tense. Such as Line 135.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

English is need improve.

Author Response

Dear Reviewer 1,  

 

Thank you for reviewing the manuscript and providing comments that contributed to the quality of the article. Regarding your suggestions and comments on this article, I will respond to each of them with a revision. The specific modifications are shown below.

 

Q1: The author should have a Figure of somatic embryogenesis process.

Feedback:

The somatic embryonic process of longan is divided into EC (embryogenic callus) ,IcpEC (incomplete compact pro-embryogenic cultures) and GE (globular embryos) stages. As you say, it is important to add a Figure of somatic embryogenesis process. In fact, the morphological changes in the somatic embryonic processes of longan have been comprehensively described in a series of previous articles in our group. This can be seen in the following papers:

 [1] Tang, M., Zhao, G., Awais, M., Gao, X., Meng, W., Lin, J., Zhao, B., Lai, Z., Lin, Y., Chen, Y., 2023. Genome-Wide Identification and Expression Analysis Reveals the B3 Superfamily Involved in Embryogenesis and Hormone Responses in Dimocarpus longan Lour. Int. J. Mol. Sci., 25(1).

[2] Tang, M., Gao, X., Meng, W., Lin, J., Zhao, G., Lai, Z., Lin, Y., Chen, Y., 2023. Transcription factors NF-YB involved in embryogenesis and hormones responses in Dimocarpus Longan Lour. Front. Plant Sci., 14, 1255436.

[3] Chen, Y., Ma, X., Xue, X., Liu, M., Zhang, X., Xiao, X., Lai, C., Zhang, Z., Lai, Z., Lin, Y., 2023. Genome-wide analysis of the SAUR gene family and function exploration of DlSAUR32 during early longan somatic embryogenesis. Plant Physiol Biochem, 195, 362-374.

Therefore, to avoid the repetition of such Figures in different papers, images of somatic embryonic processes in longan were not added to this paper.

 

Q2: Line 199, Starting from 2.5, and the paragraphs should be aligned left and right.

Feedback: I have aligned the full paragraph left and right starting at line 199, 2.5.

 

Q3: Notice to the spaces and some spellings; such as line 13; line 244.

Feedback: I have changed the spaces and some of the spelling.

 

Q4: Some need abbreviation, e.g. μM instead of μmol^-1.

Feedback: I have made changes to the unit abbreviations in the manuscript.

 

Q5: Some Latin names need to be italicized, such as Agrobacterium tumefaciens; Some English botanical names require a Latin names; such as Line176, 369-372.

Feedback: I have revised the species representation of the manuscript, and noted the italics.

 

Q6: Some grammar requires the past tense. Such as Line 135.

Feedback: I have changed the grammar to past tense.

 

In addition, all errors in the PDF have been corrected. Due to the high number of occurrences of longan in the paper, the Latin scientific name of longan has been annotated at the first occurrence of each paragraph and Figures. 

Thank you again for your meticulous review of this article to help it can be presented in a more rigorous and higher quality manner. Finally, at the time this article was revised, it was in the Chinese New Year. I would like to wish you a happy new year, best of health, and success in your research.

 

Yours sincerely,

Tingkai Zhai

 

College of Horticulture, Fujian Agriculture and Forestry University

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

Fuzhou, China

 

Reviewer 2 Report

Comments and Suggestions for Authors

Reviewer comments:

I have carefully read the manuscript ID: (plants-2863706) entitled “Genome-wide identification and expression analysis reveal 2 bZIP transcription factors mediated hormones that functions 3 during early somatic embryogenesis in Dimocarpus longan” by Zhai et al. This work presents interesting results on bZIP transcription factors identification and functions during early somatic embryogenesis in Dimocarpus longan, and the authors have presented their findings in well manner with appropriate figures. However, there are a few limitations. 

I have given my comments so that authors revise the manuscript carefully considering my comments for possible publication in “Plants”.

Abstract: Good

Introduction: Authors must give some information regarding sugar beet cultivation and production worldwide.

Line No 105: “different hormone treatment treatments” remove treatment.

Results:

Line No 125, 126: Phylogenetic tree divided into eleven sub-families and named as A, B, C, D, E, F, G, H, I, K, S. Is there any reason to select “S”?

Line No 234: Correct “The qTR-PCR results”

Authors must check and correct font for “DlbZIP” 

Line No 331: Agrobacterium must be in italics.

Line No 353, 354: Check and correct “DlbIP60”

Line 479: Check and correct "HEMMER”

Line 567: Check and correct "MS medium containing 20 g/L for” incomplete sentence.

Line No 583: Check and correct “mumbers”

Overall, it is an interesting study and should be considered for publication in Plants, once the authors address the comments and submit the revised version.

Author Response

Dear Reviewer 2,  

 

Thank you for reviewing the manuscript and providing comments that contributed to the quality of the article. Regarding your suggestions and comments on this article, I will respond to each of them with a revision. The specific modifications are shown below.

 

Introduction:

Authors must give some information regarding sugar beet cultivation and production worldwide.

Feedback:

Longan is native to southern China, and China's longan production is mainly located in Guangxi, Guangdong, Fujian and Taiwan provinces. In the world, it is mainly cultivated in countries such as China, Thailand and Vietnam. Through the search of relevant information, the cultivation and production of longan in the world were not found. Therefore, we supplemented the status of longan in horticultural plants and related cultivation in countries such as China, Thailand and Vietnam.

 

Line No 105: “different hormone treatment treatments” remove treatment.

Feedback: I have removed “treatment”.

 

Results:

Line No 125, 126: Phylogenetic tree divided into eleven sub-families and named as A, B, C, D, E, F, G, H, I, K, S. Is there any reason to select “S”?

Feedback:

In 2002, Jakoby et al. [1] first classified 75 Arabidopsis (Arabidopsis thaliana) bZIP family members into (A-I and S) 10 subfamilies using sequence similarity in the basic amino acid region as a differentiation criterion. Later, the Arabidopsis family members were updated to 78 by Droge-Laser et al. [2] on this basis (addition of bZIP76-bZIP79, exclusion of bZIP73) and expansion of the M, K, and J subfamilies. 

According to the bZIP family classification method, the phylogenetic tree can be divided into A, B, C, D, E, F, G, H, I, K, S eleven subfamilies.

[1] Jakoby, M., Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., Parcy, F., bZIP transcription factors in Arabidopsis. Trends Plant Sci 2002, 7(3), 106-11.

[2] Droge-Laser, W., Snoek, B.L., Snel, B., Weiste, C., The Arabidopsis bZIP transcription factor family-an update. Curr. Opin. Plant Biol 2018, 45(Pt A), 36-49.

 

Line No 234: Correct “The qTR-PCR results”. Authors must check and correct font for “DlbZIP”. 

Feedback: I have checked and corrected the font "DlbZIP" in the qTR-PCR results.

 

 

Line No 331: Agrobacterium must be in italics.

Feedback: I have checked and corrected the Agrobacterium tumefaciens font.

 

Line No 353, 354: Check and correct “DlbIP60”.

Feedback: I have checked and corrected the font "DlbZIP60".

 

Line 479: Check and correct "HEMMER”.

Feedback: I have checked and corrected the "HMMER".

 

Line 567: Check and correct "MS medium containing 20 g/L for” incomplete sentence.

Feedback: I have corrected this sentence.

 

Line No 583: Check and correct “mumbers”.

Feedback: I have checked and corrected the "members".

 

Thank you again for your meticulous review of this article to help it can be presented in a more rigorous and higher quality manner. Finally, at the time this article was revised, it was in the Chinese New Year. I would like to wish you a happy new year, best of health, and success in your research.

 

Yours sincerely,

Tingkai Zhai

 

College of Horticulture, Fujian Agriculture and Forestry University

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

Fuzhou, China

Reviewer 3 Report

Comments and Suggestions for Authors

The article "Genome-wide identification.....in Dimocarpus longan" by Zhai et. al identifies the bZIP transcription factors from the D. longans genome sequence, does standard bioinformatical and then additional transcriptional analysis on specific bZIP genes picked due to their expression in somatic embryogenesis and finally takes DlbZIP60 for additional characterization.  

Abstract:  line 17 - This plant is phylogenetically a eudicot; this is not an unexpected result.  

Introduction: Line 61 - Vv not Vl .  Line 64 - Ta not defined. Line 69 - Md is not defined as Malus/apple.

Paragraph starting line 82.  You should add the 3 different stages of SE that you used here.  It is only found in the material and methods.

Line 102 is not a complete sentence.

Results:  Line 134-136 does not make sense.  Reason is the same as in the abstract.  Line 146-148 point is not strong/confusing as to what you mean. Reword line 171-172 - confusing. Line 224 - pulp. Line 234 - qRT-PCR.

Changes in expression do not necessarily mean that they are playing a "vital role" line 267.  or enhance tolerance to stress - line 281.  or important role in MeJA signalling - line 290.  The Data shows expression changes - that really is all. 

Line 326 - GFP free means 'background' fluorescence.  Please explain 'airborne' in line 331 and why bacteriophage was used (a reference or more detail in material and methods.) Line 336-337 is not scientific and a 10 and 10X figure of GUS staining not needed.  Line 338 more information on amount of cells used and primers used for expression assay as it is not obvious.  Line 351 in Fig 7.  inner epidermis of onion is background.  

Discussion:  Line 387-389 In general - was there an exception of a DlbZIP being closer to a monocot than eudicot? 

Comments on the Quality of English Language

Overall, the quality of English for the paper is fine.  There were some sentences that are not grammatically correct.  Some, but not all are pointed out above.  

Author Response

Dear Reviewer 3,  

 

Thank you for reviewing the manuscript and providing comments that contributed to the quality of the article. Regarding your suggestions and comments on this article, I will respond to each of them with a revision. The specific modifications are shown below.

 

Abstract: line 17 - This plant is phylogenetically a eudicot; this is not an unexpected result.

Feedback: I have removed the reference to this result from the abstract.

 

Introduction: Line 61 - Vv not Vl. Line 64 - Ta not defined. Line 69 - Md is not defined as Malus/apple.

Feedback: I have revised the section and added the appropriate Latin names.

 

Paragraph starting line 82. You should add the 3 different stages of SE that you used here. It is only found in the material and methods.

Feedback: I have added a description of the three stages of SE in longan to this paragraph.

 

Line 102 is not a complete sentence.

Feedback: This sentence has been revised.

 

Results: Line 134-136 does not make sense. Reason is the same as in the abstract.  Line 146-148 point is not strong/confusing as to what you mean. Reword line 171-172 - confusing. Line 224 - pulp. Line 234 - qRT-PCR.

Feedback: The reference to lines 134-136 has been deleted. The point on lines 146-148 has been recorrected. I have reword the above problematic statements and words.

 

Changes in expression do not necessarily mean that they are playing a "vital role" line 267. or enhance tolerance to stress - line 281.  or important role in MeJA signalling - line 290. The Data shows expression changes - that really is all.

Feedback: I have deleted such expressions.

 

Line 326 - GFP free means 'background' fluorescence.

Please explain 'airborne' in line 331 and why bacteriophage was used (a reference or more detail in material and methods.) .

Line 336-337 is not scientific and a 10 and 10X figure of GUS staining not needed.  

Line 338 more information on amount of cells used and primers used for expression assay as it is not obvious.  

Line 351 in Fig 7. inner epidermis of onion is background.  

Feedback:

I have modified GFP(free) in line 326 to pCAMBIA1302:GFP.

I have removed the reference to 'airborne' in line 331 and also stated the type of Agrobacterium tumefaciens used in material and methods.

I have removed the unscientific presentation of lines 336-337.

For Figure 7, a-d show the GUS staining. e-h show the microscopic observation of the positive cell line at 10X magnification (for a larger field of view). i-l show the microscopic observation of the positive cell line at 20X magnification (mainly to reflect the specific morphology of the positive cells). In order to avoid any misunderstanding that the photographs were taken in a specific area, the microscopic observations at both magnifications have been placed in the figure. To explain to you the reason for the placement of the images, please reconsider whether the images at 10X magnification need to be removed, and if so, I will remove this section.

I have added 338 lines of information about the number of cells and primers used in the expression assay.

I have removed the method of stating so.

 

Discussion: Line 387-389 In general - was there an exception of a DlbZIP being closer to a monocot than eudicot?

Feedback:

So far I haven't found such an exception, and I've deleted the sentence in line 387-389.

 

Thank you again for your meticulous review of this article to help it can be presented in a more rigorous and higher quality manner. Finally, at the time this article was revised, it was in the Chinese New Year. I would like to wish you a happy new year, best of health, and success in your research.

 

Yours sincerely,

Tingkai Zhai

 

College of Horticulture, Fujian Agriculture and Forestry University

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

Fuzhou, China

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

When the plant first appeared, the scientific name was followed by a Latin scientific name such as longan (Dimocarpus longan Lour.), and then the scientific name “longan”or the abbreviation of the Latin scientific name “D. longan"; Of course, you can use the full name in the figures or tables. All Latin names are in italics.

Line 737, 1251, change "-" to "‒".

Comments on the Quality of English Language

No comment.

Author Response

Dear Reviewer 1,  

 

Thank you for once again providing valuable comments on the manuscript. The specific changes to the issues raised this time are as follows.

 

Q1: When the plant first appeared, the scientific name was followed by a Latin scientific name such as longan (Dimocarpus longan Lour.), and then the scientific name “longan”or the abbreviation of the Latin scientific name “D. longan"; Of course, you can use the full name in the figures or tables. All Latin names are in italics.

Feedback:

I have revised the nomenclature of “longan” throughout the text, by using the Latin name (Dimocarpus longan Lour.) for the first time. Subsequent appearances used D. longan.

 

Q2: Line 737, 1251, change "-" to "‒".

Feedback: I have changed "-" to "‒".

 

Thank you again for your careful review of this manuscript.

 

Yours sincerely,

Tingkai Zhai

 

College of Horticulture, Fujian Agriculture and Forestry University

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

Fuzhou, China

 

Reviewer 3 Report

Comments and Suggestions for Authors

Edits in line 330-332 are unclear.  Are they describing expression numbers or splicing of genes?  Line 333-335 also unclear.  How can members of a family of genes be detected (maybe not the correct word) via the UTR? Members of a gene family are detected via protein/domain similarity.  Line 498 - still spelling the tissue type incorrectly.  Line 703 not a sentence. Line 736-739 belongs in material and methods.  

Once a genus/species has been identified (Oryza sativa - rice), it does not need to be stated over multiple times unless that is a requirement of this journal.  If not - once is enough.

Comments on the Quality of English Language

Comments above 

Author Response

Dear Reviewer 3,  

 

Thank you for once again providing valuable comments on the manuscript. The specific changes to the issues raised this time are as follows.

 

Q1: Edits in line 330-332 are unclear. Are they describing expression numbers or splicing of genes? 

Q2: Line 333-335 also unclear. How can members of a family of genes be detected (maybe not the correct word) via the UTR? Members of a gene family are detected via protein/domain similarity. 

Q3: Line 498 - still spelling the tissue type incorrectly. 

Q4: Line 703 not a sentence.

Q5: Line 736-739 belongs in material and methods.

Q6: Once a genus/species has been identified (Oryza sativa - rice), it does not need to be stated over multiple times unless that is a requirement of this journal.  If not - once is enough.

 

Feedback:

Q1 and Q2: I have reanalysed this paragraph.

Q3: The word "pulp" in line 498 has been corrected.

Q4: The expression for line 703 has been amended.

Q5: The passage has moved to material and methods.

Q6: I have made changes to this issue.

 

Thank you again for your careful review of this manuscript.

 

Yours sincerely,

Tingkai Zhai

 

College of Horticulture, Fujian Agriculture and Forestry University

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University

Fuzhou, China