Genome-Wide Identification and Characterization of TCP Genes in Eight Prunus Species and Their Expression Patterns Under Cold Stress in P. tenella var. tenella
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript with the title “Genome-Wide Identification and Characterization of TCP genes in Eight Prunus Species and Their Expression Patterns Under Cold Stress in P. nana” provides the first genome-wide study of the TCP gene family in eight Prunus species. The manuscript is highly novel. Below I give my comments and suggestions for improvement.
Results
The Figure 2 is impossible to read, I recommend to be enlarged.
Supplementary
The manuscript is referring to “Supplementary Data S1”, Table S1, but I not find such a document.
Material and method
This section should contain a chapter dedicated to plant/biologic material. Now this is completely lacking. I must stress out that it is important to mention the source of these plant materials used (Prunus nana, P. dulcis, P. armeniaca, P. fruticose, P. kanzakura, P. mira, P. mume var. tortuosa, P. yedoensis), clarify taxonomy used and if any of these were cultivars (particularly considering that the manuscript hints to importance in plant breeding it must be known this). Possibly vouchers code of plants would have been excellent as well. Please note that the entire work is based on the presumption that species and plant material used was accurately assigned, an important fact in support of the usefulness of the findings reported here.
Taxonomy
Important – names of species should be verified with IPNI or other reputable database to ensure the spelling of these is scientifically accurate. Otherwise if names are not accurate the results become less useful, the paper might be less likely to be found when other researchers search for these species and implicitly the chances of the paper to be cited.
Example: Prunus nana is a recognized taxon of wild almond? Please note Amygdalus nana is now Prunus tenella var. tenella if is refereeing to wild almond. This is why accurate taxonomy is important. A large portion of the manuscript refers to this species (P. nana) and things must be clarified in this regard.
References
The list of reference must be updated with most recent literature. The manuscript is poorly connected with recent research on the topic – out of 42 cited sources none are from 2024, one from 2023, and 3 from 2022.
Best regards.
Comments on the Quality of English LanguageEnglish
Moderate improvements of English style and grammar are recommended. Also correcting typing errors and spelling is a must.
Line 51 “ornamentals plants” should be “ornamental plants” without s
Line 61 “fice subgenera” should be “five subgenera” with v instead of c
Etc.
Author Response
The manuscript with the title “Genome-Wide Identification and Characterization of TCP genes in Eight Prunus Species and Their Expression Patterns Under Cold Stress in P. nana” provides the first genome-wide study of the TCP gene family in eight Prunus species. The manuscript is highly novel. Below I give my comments and suggestions for improvement.
Results
The Figure 2 is impossible to read, I recommend to be enlarged.
RESPONSE: Thank you. We have enlarged the Figure 2.
Supplementary
The manuscript is referring to “Supplementary Data S1”, Table S1, but I not find such a document.
RESPONSE: Thank you. We have supplemented these documents.
Material and method
This section should contain a chapter dedicated to plant/biologic material. Now this is completely lacking. I must stress out that it is important to mention the source of these plant materials used (Prunus nana, P. dulcis, P. armeniaca, P. fruticose, P. kanzakura, P. mira, P. mume var. tortuosa, P. yedoensis), clarify taxonomy used and if any of these were cultivars (particularly considering that the manuscript hints to importance in plant breeding it must be known this). Possibly vouchers code of plants would have been excellent as well. Please note that the entire work is based on the presumption that species and plant material used was accurately assigned, an important fact in support of the usefulness of the findings reported here.
RESPONSE: Thank you for the valuable suggestions. We have added "2.1 Taxon sampling" to the Materials and Methods section, providing detailed information on the sources of the genomes used in the study and the basis for updating the scientific names of each species.
Taxonomy
Important – names of species should be verified with IPNI or other reputable database to ensure the spelling of these is scientifically accurate. Otherwise if names are not accurate the results become less useful, the paper might be less likely to be found when other researchers search for these species and implicitly the chances of the paper to be cited.
Example: Prunus nana is a recognized taxon of wild almond? Please note Amygdalus nana is now Prunus tenella var. tenella if is refereeing to wild almond. This is why accurate taxonomy is important. A large portion of the manuscript refers to this species (P. nana) and things must be clarified in this regard.
RESPONSE: Thank you, all the species names have been verified with POWO, and the names have been updated throughout the manuscript; the species names in Tables and Figure 2, Figure 3, and Figure 4 have also been updated. Regarding Prunus tenella var. tenella (the synonym Prunus nana and Amygdalus nana), which is sourced from the Xinjiang province of China, it shows significant differences in height, fruit shape, fruit pubescence, and the surface texture of the endocarp compared to the closely related species Prunus davidiana var. davidiana. We can ensure the accuracy of the sample identification, please find in the Figure S1.
References
The list of reference must be updated with most recent literature. The manuscript is poorly connected with recent research on the topic – out of 42 cited sources none are from 2024, one from 2023, and 3 from 2022.
Response: Thanks. We’ve updated the references. Additional references are as follows:
Zhao, J.; He, Z.; Fang, S.; Han,X.; Jiang, L.; Hu, Y.; Yu, H.; Zhang, L.; Zhou, X. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. Front. Plant Sci., 2024,15:1404071.
Cheng, P.; Bi, D.; Chen, J.; Zhao, M.; Wang, Y.; Wang, H.; Cao, P.; Huang, C. Genome-wide identification and analysis of TCP transcription factor genes in Rosa chinensis in response to abiotic stress and fungal diseases. Ornamental Plant Research 2023, 3:0003.
Yao, Y.; Dong, L.; Fu, X.; Zhao, L.; Wei, J. et al. HrTCP20 dramatically enhance drought tolerance of sea buckthorn (Hippophae rhamnoides L). by mediating the JA signaling pathway. Plant Physiology and Biochemistry 2022 174:51−62.
Hur, Y.S.; Oh, J.; Namuk, K.; et al. Arabidopsis transcription factor TCP13 promotes shade avoidance syndrome-like responses by directly targeting a subset of shade-responsive gene promoters. Journal of Experimental Botany 2024, 75(1):241-257.
Pan, Z.; Qiulin, Y.; Yumei, H. et al. PagHAM4a-PagSCL21 and PagHAM4b-PagTCP20 modules positively regulate cambial activity and its differentiation into secondary xylem in poplar. Journal of Experimental Botany 2024, erae375.
Li, C.; Zhang, L.; Li, H. et al. BrrTCP4b interacts with BrrTTG1 to suppress the development of trichomes in Brassica rapa var. rapa. Plant Diversity 2024, 46(3):416-420.
English
Moderate improvements of English style and grammar are recommended. Also correcting typing errors and spelling is a must.
Line 51 “ornamentals plants” should be “ornamental plants” without s
Line 61 “fice subgenera” should be “five subgenera” with v instead of c
Etc.
Response: Thank you. We have checked and corrected the grammatical and spelling errors in the manuscript.
Figures 1 and 2 have low resolution, but since I only have the pdf of the manuscript I don’t know if it is because of the pdf format. Please check that in word document the resolution is sufficient to magnify and read the letters in figures 1 and 2 (because in the pdf it is very hard to read the letters due to low resolution). Please check all the subsequent figures for resolution
Response: Thank you. We have enlarged the Figure 1 and Figure 2.
Reviewer 2 Report
Comments and Suggestions for AuthorsDear authors,
Please go through the manuscript and check internet links you provided for web tools used. Some of them have extra spaces or characters in them, and when copied or used directly from the pdf do not lead to web page intended. Please try every one of them and fix this. (example is the link in line 102 and the link in the line 100)
Line 71. A few references to back up the sentence is needed.
Line 1260. Different font was used for the word Among
Figures 1 and 2 have low resolution, but since I only have the pdf of the manuscript I don’t know if it is because of the pdf format. Please check that in word document the resolution is sufficient to magnify and read the letters in figures 1 and 2 (because in the pdf it is very hard to read the letters due to low resolution). Please check all the subsequent figures for resolution
Author Response
Please go through the manuscript and check internet links you provided for web tools used. Some of them have extra spaces or characters in them, and when copied or used directly from the pdf do not lead to web page intended. Please try every one of them and fix this. (example is the link in line 102 and the link in the line 100)
Response: Thank you. We have checked and renewaled the internet links in manuscript.
Line 71. A few references to back up the sentence is needed.
Response：Thank you. We have added references.
Line 1260. Different font was used for the word Among
Response: Thank you. We have corrected it.
Figures 1 and 2 have low resolution, but since I only have the pdf of the manuscript I don’t know if it is because of the pdf format. Please check that in word document the resolution is sufficient to magnify and read the letters in figures 1 and 2 (because in the pdf it is very hard to read the letters due to low resolution). Please check all the subsequent figures for resolution
Response: Thank you. We have enlarged the Figure 1 and Figure 2.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsDear authors,
all comments were resolved and the changes significantly improved the manuscript.
Best regards.
