DNA Barcode and Correct Scientific Name of Golden Pompano, an Important Marine Aquaculture Fish Species in China

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript title “DNA barcode and correct scientific name of Golden Pompano, an important marine aquaculture fish species in China” is very interesting. However, it needs to be revised as follows:

In the FishBase database, if authors enter the common name “Golden Pompano”, no exact match is found. However, if authors enter the scientific name Trachinotus ovatus, the common name appears as “Pompano” and other names that do not include “Golden Pompano”. The authors should provide further discussion on this content.

Provide BOLD/GenBank accession numbers of 36 COI sequences from this study.

Line 47: Revise to “292,263 tons”.

Line 52: Revise to “…,in "Marine Fishes of Southern Fujian, China" (2014) [5],…” and delete [5] in Line 54.

Line 54: Revise to “In "key to Marine and Estuarial Fishes of China" (2021) [6],…” and delete [6] in Line 56.

Line 72: Revise to “…many species of the genus Trachinotus”.

Line 92: Please check YJ1-YJ12?

Line 104: Provide the full term of COI, due to the first mention.

Line 107-108: The total volume of all PCR reagents did not 25 µl, please check.

Line 118: Provide reference for Librado & Rozas 2009 in [?].

Line 122: Revise to “…MEGA X [18] with…” and delete [18] in Line 124.

Table 1: Zhang et al., 2016a [22] and Zhang et al., 2016b [25], is it necessary to include a and b?

Figure 2: Why didn't the authors construct phylogenetic tree for only Trachinotus ovatus from the 36 nucleotide sequences of this study and the 12 sequences from the database, so that it would be clear that Trachinotus ovatus samples from this study come from Indo-west Pacific?

Figure 2: Provide the description of scale bar.

Line 158: KM245969 was not present in Table1.

Line 162: Chang Table 1 to Figure 2.

Line 174: Chang hap5 to hap3, please check.

Author Response

Response letter to the reviews

Dear Editors and Reviewers,

Thank you very much for your intensive editing work on our manuscript entitled “DNA barcode and correct scientific name of Golden Pompano, an important marine aquaculture fish species in China” (Manuscript ID: fishes-3504071) and giving us the opportunity to revise and resubmit it. At the same time, we appreciate the insightful comments of the three reviewers, which are valuable and have helped us to improve the quality of our manuscript.

We have carefully considered the reviewers’ comments and suggestions and have made the necessary revisions and supplement. In response to different reviewers, we highlighted the modified content with different font colors, highlighting the modifications of Reviewer 1’s comments in red font and Reviewer 3’s comments in blue font. All the above modifications were also made in response to the comments from Reviewer 2. In addition, the changed reference numbers due to manuscript modifications were highlighted in purple font.

We hope that the revision is acceptable, and I look forward to hearing from you soon.

With best regards,

Yours sincerely,

Ang Li and Shufang Liu

March 3, 2025

 

The specific responses to each reviewers are as follows： 

To Reviewer 1:

Comments 1:

In the FishBase database, if authors enter the common name “Golden Pompano”, no exact match is found. However, if authors enter the scientific name Trachinotus ovatus, the common name appears as “Pompano” and other names that do not include “Golden Pompano”. The authors should provide further discussion on this content.

Response 1:

“Golden Pompano” (the literal English translation of the Chinese pronunciation “Jin Chang”) is the most widely used common name for the main cultured species of pompano in China (and is also the research subject of this study), although this name is not used by FishBase. Therefore, this study retains the use of “Golden Pompano” to refer to the research subject. The species “Golden Pompano” does not appear in FishBase, and the so-called “Trachinotus ovatus” in FishBase (common name: Pompano) corresponds to the “East Atlantic type” of Trachinotus ovatus in this study. The above content was mentioned in the “introduction” of the manuscript.

 

Comments 2:

Provide BOLD/GenBank accession numbers of 36 COI sequences from this study.

Response 2:

We accepted the suggestion and provided GenBank accession numbers (PV164038-PV164042) for all five haplotypes of the 36 COI sequences in the “results” of the manuscript.

 

Comments 3:

Line 47: Revise to “292,263 tons”.

Response 3:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 4:

Line 52: Revise to “…, in "Marine Fishes of Southern Fujian, China" (2014) [5],…” and delete [5] in Line 54.

Response 4:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 5:

Line 54: Revise to “In "key to Marine and Estuarial Fishes of China" (2021) [6],…” and delete [6] in Line 56.

Response 5:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 6:

Line 72: Revise to “…many species of the genus Trachinotus”.

Response 6:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 7:

Line 92: Please check YJ1-YJ12?

Response 7:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 8:

Line 104: Provide the full term of COI, due to the first mention.

Response 8:

According to the reviewer’s comments, we have supplemented the full name of COI gene (cytochrome c oxidase subunit I gene).

 

Comments 9:

Line 107-108: The total volume of all PCR reagents did not 25 µl, please check.

Response 9:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 10:

Line 118: Provide reference for Librado & Rozas 2009 in [?].

Response 10:

According to the reviewer’s comments, we have supplemented the reference.

 

Comments 11:

Line 122: Revise to “…MEGA X [18] with…” and delete [18] in Line 124.

Response 11:

According to the reviewer’s comments, corresponding modifications have been made.

 

Comments 12:

Table 1: Zhang et al., 2016a [22] and Zhang et al., 2016b [25], is it necessary to include a and b?

Response 12:

According to the reviewer’s comments, corresponding modifications have been made (deleted the “a” and “b”).

 

Comments 13:

Figure 2: Why didn't the authors construct phylogenetic tree for only Trachinotus ovatus from the 36 nucleotide sequences of this study and the 12 sequences from the database, so that it would be clear that Trachinotus ovatus samples from this study come from Indo-west Pacific?

Response 13:

In this study, we constructed phylogenetic trees for 16 pompano species (genus Trachinotus) and their sibling species, Lichia amia. The primary purpose was to determine which particular Trachinotus species the “golden pompano” represents. Therefore, all species related to the names “golden pompano” and “T. ovatus” (including the Indo-West Pacific type and the East Atlantic type) were used as reference sequences for phylogenetic analysis. Furthermore, through the construction of the phylogenetic tree, we attempted to clarify the phylogenetic relationships between the two species related to the name “T. ovatus” and to determine whether they could form phylogenetically distant and distinct monophyletic clades.

 

Comments 14:

Figure 2: Provide the description of scale bar.

Response 14:

According to the reviewer’s comments, we have supplemented the description of scale bar for Figure 2.

 

Comments 15:

Figure 2: Line 158: KM245969 was not present in Table1.

Response 15:

According to the reviewer’s comments, we checked the manuscript and confirmed that Table 2 already included the information for KM245969.

 

Comments 16:

Line 162: Change Table 1 to Figure 2.

Response 16:

According to the reviewer’s comments, we have supplemented the annotations of “Figure 2 and Figure 3” in the appropriate positions. We retained the annotations of “Table1” because it provides geographical information about the sequence origins.

 

Comments 17:

Line 174: Change hap5 to hap3, please check.

Response 17:

According to the reviewer’s comments, we checked the five haplotypes and found that “hap3” is not a “shared haplotype”, while the haplotype “hap5” is shared by four golden pompano samples we collected (FCG6, ZZ7, ND1, ND3) and the reference sequence KY802069. Therefore, we did not make any changes here.

 

Reviewer 2 Report

Comments and Suggestions for Authors

The study is too simple and limited for an original publication. It could be a short communication in a journal focused on aquaculture. Few individuals were analyzed and all of them were from farms.
The authors should use a nuclear marker to complement the data.
The graph in Figure 2 should be presented in more detail, also adding the BIN information.
The authors may consider, for future publications, presenting the images of the fish next to the species groups.

Author Response

Response letter to the reviews

Dear Editors and Reviewers,

Thank you very much for your intensive editing work on our manuscript entitled “DNA barcode and correct scientific name of Golden Pompano, an important marine aquaculture fish species in China” (Manuscript ID: fishes-3504071) and giving us the opportunity to revise and resubmit it. At the same time, we appreciate the insightful comments of the three reviewers, which are valuable and have helped us to improve the quality of our manuscript.

We have carefully considered the reviewers’ comments and suggestions and have made the necessary revisions and supplement. In response to different reviewers, we highlighted the modified content with different font colors, highlighting the modifications of Reviewer 1’s comments in red font and Reviewer 3’s comments in blue font. All the above modifications were also made in response to the comments from Reviewer 2. In addition, the changed reference numbers due to manuscript modifications were highlighted in purple font.

We hope that the revision is acceptable, and I look forward to hearing from you soon.

With best regards,

Yours sincerely,

Ang Li and Shufang Liu

March 3, 2025

 

The specific responses to each reviewers are as follows： 

To Reviewer 2:

Comments 1:

The study is too simple and limited for an original publication. It could be a short communication in a journal focused on aquaculture. Few individuals were analyzed and all of them were from farms.

Response 1:

Thank you for the insightful comments, which are valuable for improving the quality of our manuscript. In this study, we focus on the commercially important fish species, golden pompano, which ranks at the top of production in China's current marine fish aquaculture. Extensive samplings were conducted, encompassing the primary production regions (four provinces) of golden pompano in China. We attempted to address the long-standing controversy regarding the species delimitation of golden pompano for China's mariculture industry, rather than merely dealing with a taxonomic issue. We are convinced that this work is essential and significant for the sustainable development of golden pompano resources and sincerely hope to publish it in the form of a research paper.

 

Comments 2:

The authors should use a nuclear marker to complement the data.

Response 2:

Thank you for pointing this out. In recent years, DNA barcoding has been suggested as an effective technique for species delimitation. Considering that extensive DNA barcode data for pompano (genus Trachinotus) have already been accumulated, we attempted to employ DNA barcoding in this study, and the reference sequences were strictly selected by prioritizing which had been documented or published to ensure accuracy. The results of multiple analyses indicated that accurate species delimitation of the golden pompano could be achieved by DNA barcoding. In future study, we will supplement the nuclear marker data to further substantiate our conclusions.

 

Comments 3:

The graph in Figure 2 should be presented in more detail, also adding the BIN information.

Response 3:

According to the reviewer’s comments, we have supplemented some details in Figure 2. In this figure, the BOLD BIN or GenBank accession number of the reference sequences are shown. More specific information about them was presented in Table 1. In addition, we have supplemented our work with Bayesian phylogenetic inference, ABCD, and bPTP analyses to highlight species delimitation. The relevant contents have been added to the manuscript.

 

Comments 4:

The authors may consider, for future publications, presenting the images of the fish next to the species groups.

Response 4:

According to the reviewer’s comments, we have collected some relevant images. However, some of them do not meet the requirements for scientific publication. We will continue to collect and provide the images in further study.

 

Reviewer 3 Report

Comments and Suggestions for Authors

The authors presented an interesting case of taxonomical confusion regarding the golden pompano, an important commercial species in Chinese aquaculture, clearly resolved by using a powerful tool as DNA barcoding. Along with this, the authors demonstrated that DNA barcoding remains a valuable instrument at the service of biodiversity conservation.

I recommend this manuscript to be published with some extra (non-invasive) data analysis to confirm the results and strengthen the manuscript (the discussion mostly).

1) Supposing that the brand new COI sequences (36) and relative voucher data have been published on BOLD and NCBI by the authors (there is no mention about this in M&M or Results sections, so please, consider to do that asap if you did not arrange for it in the meantime) , I suggest to take advantage of BOLD systems with a BIN analysis.

2) I would suggest to confirm the results with Bayesian approaches aiming at highlighting species delimitation (using ABGD and bPTP methods).

A very minor comment to the title (Line 2): the authors refer to "Golden Pompano"", while in the main tex to "golden pompano". Please, consider adapting the title to the text style.

Author Response

Response letter to the reviews

Dear Editors and Reviewers,

Thank you very much for your intensive editing work on our manuscript entitled “DNA barcode and correct scientific name of Golden Pompano, an important marine aquaculture fish species in China” (Manuscript ID: fishes-3504071) and giving us the opportunity to revise and resubmit it. At the same time, we appreciate the insightful comments of the three reviewers, which are valuable and have helped us to improve the quality of our manuscript.

We have carefully considered the reviewers’ comments and suggestions and have made the necessary revisions and supplement. In response to different reviewers, we highlighted the modified content with different font colors, highlighting the modifications of Reviewer 1’s comments in red font and Reviewer 3’s comments in blue font. All the above modifications were also made in response to the comments from Reviewer 2. In addition, the changed reference numbers due to manuscript modifications were highlighted in purple font.

We hope that the revision is acceptable, and I look forward to hearing from you soon.

With best regards,

Yours sincerely,

Ang Li and Shufang Liu

March 3, 2025

 

The specific responses to each reviewers are as follows： 

To Reviewer 3:

Comments 1:

Supposing that the brand new COI sequences (36) and relative voucher data have been published on BOLD and NCBI by the authors (there is no mention about this in M&M or Results sections, so please, consider to do that asap if you did not arrange for it in the meantime), I suggest to take advantage of BOLD systems with a BIN analysis.

Response 1:

We accepted the suggestion and provided GenBank accession numbers (PV164038-PV164042) for all five haplotypes of the 36 COI sequences in the “results” of the manuscript. The reference sequences from BOLD had been directly used in comparative studies with the sequences obtained in this study, including the analyses of shared haplotypes, genetic distances, and phylogenetic relationships.

 

Comments 2:

I would suggest to confirm the results with Bayesian approaches aiming at highlighting species delimitation (using ABGD and bPTP methods).

Response 2:

According to the reviewer’s comments, we have supplemented our work with Bayesian phylogenetic inference, ABCD, and bPTP analyses to highlight species delimitation. The relevant contents have been added to the manuscript.

 

Comments 3:

A very minor comment to the title (Line 2): the authors refer to “Golden Pompano”, while in the main text to “golden pompano”. Please, consider adapting the title to the text style.

Response 3:

According to the reviewer’s comments, corresponding modifications have been made.

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

Thank you to the authors for the new analysis performed.

The manuscript is complete. I recommend its publication.

Author Response

                                                      Response letter to the Reviewer 3

Dear Reviewer,

Thank you for your recognition of our manuscript. We appreciate the insightful comments, which are valuable and have helped us to improve the quality of our manuscript.

With best regards,

Yours sincerely,

Ang Li and Shufang Liu

March 13, 2025