Characterization and Phylogenetic Analysis of the First Complete Mitochondrial Genome of Gnathophyllum americanum (Guérin-Méneville, 1855) (Malacostraca: Decapoda: Palaemonidae)

Round 1

Reviewer 1 Report

This paper provides important information for mitochondrial DNA research in Decapoda Crustacea.

L. 36: Spell out G. Americanum

L. 45-46: “The complete mitogenome DNA sequence is 11–20 kb in length.” No reference? I suppose some metazoans possess mtDNA larger than this.

L. 50: Is the reference [4] Liu et al. (2912) plausible for this?

L. 136-137: Ye et al. (2021) [13] is not the first to mention that Exopalaemon is nested in the genus Palaemon. See Kou et al. (2013) (Invertebrate Systematics 27: 502-514).

L. 157-158: may be “the genera Gnathophyllum and Hymenocera share common ancestor”.

Author Response

1. Thank you for your comment. We have revised it.
2. Thank you for your comment. We have cited a new paper and correctd it in our manuscript.
3. We have corrected it.
4. We have cited and added the proposed paper in our reference.
5. We have revised as the reviewer suggested.

Reviewer 2 Report

This study aimed to characterize the mitogenome of G. americanum, and phylogenetic analyses d the phylogenetic relationships of 23 Decapoda species. Although the findings of this research provide some important data for the complete mitogenome of this decapod species, more information regarding the characterization and phylogeny:

1.       Some information regarding the necessity of the complete mitogenome of this species regarding the phylogeny of decapod species and their limitations could be better to set your hypothesis.

2.       The aim of the study should be clearly stated before giving the significance of the study. Moreover, this sentence, “To better understand G. americanum at the DNA molecular level, we promoted the development of species identification, population genetics, and biogeography” must be revised since no information is provided about species identification, population genetics and biogeography in this study.

3.       Each gene’s start and stop codon is not given; the most common ones are given.

4.       It would be better to provide the secondary structure of tRNAs, 16S rRNA and 12S rRNA and their domains in the G. americanum predicted against the known rRNA secondary structures.

5.       Description of non-coding sequences is not provided. For example, the length and location of the non-coding regions could have been described.

6.       More description of the mitogenome sequencing conditions, their assembly, and the primers used for mitogenome analyses are needed.

7. Phylogenetic relationships were constructed based on the 13 protein-coding gene sequences. Why were the other regions of mitogenome not included in the phylogenetic analyses? It would have been better to make a few data sets, such as nucleotide and amino acid sequences of 13 protein-coding genes and nucleotide sequences of two rRNAs.

Author Response

1. Thank you for your comment. We made some revision and we stressed that the MGO (mitochondrial gene order) of G. americanum and Hymenocera picta is unique in Decapoda. Both the phylogeny based on mitochondrial genomic DNA data and the unique MGO pattern indicate the genus Gnathophyllum might be sister to the genus Hymenocera.
2. We have revised it. Thank you .
3. In the Table 1, We listed all the information of start and stop codonfor each protein coding gene.
4. Thank you for your suggestion. We have added the secondary structure of every  tRNA in Figure 4. Because the type of this paper is “Communication”, we are afraid not to include 16S rRNA and 12S rRNA .
5. We have added the description of non-coding sequence in the manuscript. Thank you.
6. We have revised it in the method part of our manuscript. We didn’t use PCR, so no primer was used in our study.
7. We have added 16S and 12s rRNA and conbined with 13PCG as the dataset for reanalyses and revised it in the manuscript. Thank you for your comments.

Reviewer 3 Report

The ms entitled "Characterization and phylogenetic analysis of the first complete mitochondrial genome of Gnathophyllum americanum (Guérin-Méneville, 1855) (Malacostraca: Decapoda: Palaemonidae)" aims to  to sequence and characterize the complete mitogenome of the G.americanum species.

 

The ms is well written and definitely important for the phylogeny aspect of the studied species. 

I have some suggestion for the authors as listed below:

Introduction

Point_1: The authors should stress out the importance of sequencing the mitogenome of the G.americanum and give an extended insight with respect to species phylogeny. For instance, is their phylogeny controvesial? Are species of the Gnathophyllum genus that are likely to represent complexes that require a deeper taxonomic resolution?

M&Ms

Point_2: I propose the authors to refer how they did confirm the quality of the assembly, correct potential assembly gaps, and finally close the circular molecule. (e.g. total DNA-seq reads were mapped to the assembled mitogenome from the same species with Geneious Prime?)

Point_3: It might be worth running the phylogenetic approach using also Bayesian Inference  (MrBayes software) for cross-checking of the output tree? Just a suggestion.

Results

The authors could also discuss their findings with respect to monophylies, paraphylies etc, to give a more comprehensive soundness of their findings.

 

Thus, I propose the acceptance for publication of the present ms, after they consider/reply to my suggestions.

Author Response

1. Thank you for your comment. 10 species was described in the genus Gnathophyllum. This is the first complete Mitogenome for the genus Gnathophyllum and for the species G. americanum .  We have tried to stress on the importance of the information of this genome, especially we found that the MGO (mitochondrial gene order) of G. americanum and Hymenocera picta is unique in Decapoda. Both the phylogeny based on mitochondrial genomic DNA data and the unique MGO pattern indicates the genus Gnathophyllum might be sister to the genus Hymenocera. G.americanum is widely distributed in North Atlantic Ocean, aribbean Sea, Gulf of Mexico, South Pacific Ocean, Mozambique Channel, Red Sea, Indian Ocean. We believe this study will be useful for molecular phylogeny of Gnathophyllum and population genetics and molecular biogeography of G. americanum in the future.
2. We have revised some in Method part. If the mitogenome can’t be assembled into a single contig, we use PCR and sanger sequencing to check the potential gap and orientation. In this study, the G. americanum mtDNA was assembled into a single contig. We used cox1 gene to confirm the location and orientation, and mapped the trimmed reads to the single contig. After mapping analysis, we can evaluate the reads distribution and assembling efficiency. The assembling coverage of G. americanum is 70X. The software we used is the CLC Genomics workbench v20.

 

3. Thank you for your comment. The bootstrap values in every clade were high enough for support this topology in our analysis, so we didn’t try to reanalyze the data using BI.
4. We have tried to stress on the importance of the information of this genome, especially we found that the MGO (mitochondrial gene order) of G. americanum and Hymenocera picta is unique in Decapoda. Both the phylogeny based on mitochondrial genomic DNA data and the unique MGO pattern indicates the genus Gnathophyllum might be sister to the genus Hymenocera. The families Palaemonidae, Alvinocarididae, Atyidae, Nephropidae, Penaeidae, Rhynchocinetidae and Callianassidae were monophyletic.

 

Round 2

Reviewer 2 Report

The manuscript has been revised according to my comments but there are some points still needed to be checked carefully and revised: 

1. Line 137: Figure 1 is given as Fig. 1. 

2. Line 150: Figure 4 should be Figure 5. 

3. It has been stated that "13 protein-coding, 16S ribosomal RNA and 12S ribosomal RNA genes" has been used for phylogeny construction, but in Figure 5 caption is different, saying that it is "based on the DNA sequence of 13  protein-coding and two rRNA genes." 

Author Response

      Thank you for your useful comments.

1. We have corrected it. Thank you.
2. We have corrected it.
3. We have revised our manuscript as you suggested.