The complete mitochondrial genome Hainan Gymnure,&nbsp;<i>Neohylomys hainanensis</i>

Feiyun Tu; Xiaodan Hou; Qiujie Lu; Xiaofei Zhai

doi:10.12688/f1000research.131600.2

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Genome Note

Revised

The complete mitochondrial genome Hainan Gymnure, Neohylomys hainanensis

[version 2; peer review: 2 approved with reservations]

Feiyun Tu ¹, Xiaodan Hou¹, Qiujie Lu¹, Xiaofei Zhai¹

PUBLISHED 20 Oct 2025

Author details Author details

¹ Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

Feiyun Tu
Roles: Conceptualization, Formal Analysis, Funding Acquisition, Resources, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing

Xiaodan Hou
Roles: Investigation, Methodology, Software, Validation, Visualization

Qiujie Lu
Roles: Methodology, Software

Xiaofei Zhai
Roles: Data Curation, Investigation

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Abstract

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N . hainanensis is closely related to Neotetracus sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

Keywords

Neohylomys hainanensis, mitochondrial genome, phylogeny, Erinaceidae

Corresponding author: Feiyun Tu

Competing interests: No competing interests were disclosed.

Grant information: The study was supported by the project of the Natural Science Foundation of Hainan Province [No. 321RC544].
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2025 Tu F et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Tu F, Hou X, Lu Q and Zhai X. The complete mitochondrial genome Hainan Gymnure, Neohylomys hainanensis [version 2; peer review: 2 approved with reservations]. F1000Research 2025, 12:294 (https://doi.org/10.12688/f1000research.131600.2) First published: 16 Mar 2023, 12:294 (https://doi.org/10.12688/f1000research.131600.1) Latest published: 20 Oct 2025, 12:294 (https://doi.org/10.12688/f1000research.131600.2)

Revised Amendments from Version 1

The article has been revised following two reviewers' comments and suggestions. The readability of the article has been improved.

See the authors' detailed response to the review by Michael Allen
See the authors' detailed response to the review by Perinçek Seçkinozan Şeker

Introduction

The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a small mammal distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Liu and Wu 2019; Shaw et al. 1966; Smith et al. 2009; Abramov et al. 2018). In China, eight species are currently recognized within the family Erinaceidae (Smith et al. 2009). However, the phylogenetic relationships of three species (N. hainanensis, Hylomys suillus and Neotetracus sinensis) within Erinaceidae have been debated (Cobert 1988; Gould 1995; Grenyer and Purvis 2003; He et al. 2012). Previous studies (Cobert 1988; Gould 1995; Grenyer and Purvis 2003) indicated sister relationships of N. hainanensis and N. sinensis based on morphological data. However, He et al. (2012) showed that N. sinensis clustered with H. suillus rather than N. hainanensis based on combined data of mitochondrial genes (CYTB, ND2 and 12S). Complete mitochondrial genome sequences are highly informative markers for resolving phylogenetic relationships among taxa (Kumazawa 2007; Shen et al. 2010; Yue et al. 2015). Though the complete mitochondrial genome of N. hainanensis is available in GenBank (MW429379), we sequenced the mitochondrial genome using our sample based on primer walking method to confirm the accuracy of the data. Additionally, we investigated phylogenetic relationships of N. hainanensis among family Erinaceidae in an attempt to resolve the current phylogenetic disputes.

Methods

The animal was captured using a mouse cage trap at Yinggeling Mountains (109.289°E, 18.878°N), Hainan province, China in May, 2022. The animal was euthanized in a 10 L euthanasia chamber, which was gradually filled with 99% purity of CO₂ within 2-3 minutes.

A total of 2 g of femoral muscle sample was clipped from the specimen using surgical scissors, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989), which contained three main procedures: 1) Sodium dodecylsulfate (SDS) and proteinase K were used for the enzymatic digestion of proteins; 2) A mixture of phenol: chloroform:isoamyl alcohol (25:24:1) was then added to promote the partitioning of lipids into the organic phase; 3) The DNA was rinsed using analytical alcohol of different solubility and then otained the purified DNA for PCR. Seven primer combinations were used for the generation of PCR products (see Extended data (Tu 2023)). PCR amplifications of mitochondrial genome of N. hainanensis were listed as follows: PCR amplifications were carried out in 25 uL reaction volumes containing 1×^EX Taq buffer (Mg²⁺ Free; TaKaRaBiotech, Dalian, China), 2.5 mM MgCl₂, 0.1-0.4 mM dNTP, 0.4 uM each primer, 0.04 u/uL ^EX Taq polymerase, and ~5 ng/uL total genomic DNA as template. PCR protocol was set as follows: an initial denaturation at 94°C for 4 min; 35 cycles of amplification as the main procedure: a denaturation at 94°C for 45 s, an annealing at 50-60°C for 50 s, an elongation at 72°C for 2-3 min, and a final extension at 72°C for 4 min. All PCR products were examined through electrophoresing on a 1.0% agarose gel and then directly sequenced using an ABI 3730xl sequencer. The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files. The boundaries of protein-coding genes were predicted via comparison with homologs using MEGA 6.0 (Tamura et al. 2013). The transfer RNA (tRNA) genes were identified using tRNAscan-SE 2.0 (Lowe and Chan 2016).

To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Results

The whole mitochondrial genome of N. hainanensis is 17,337 bp in length (GenBank Accession number ON054206.2 (Tu and Hou 2022)) and contains 13 protein-coding genes (PCGs), 22 tRNAs genes, two rRNAs genes, and one control region. The base composition of N. hainanensis mitogenome is as follows: A 33.4%, G 12.2%, T 33.1%, and C 21.3%. Typically, an A+T rich pattern (66.5%) was observed. Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp). Within 37 mitochodrial genes, the ND6 gene and eight tRNAs (tRNA ^Gln, tRNA ^Ala, tRNA ^Asn, tRNA ^Cys, tRNA ^Tyr, tRNA ^Ser, tRNA ^Glu and tRNA ^Pro) were encoded on the L-strand, whereas all other genes were encoded on the H-strand. Most mitochondrial PCGs, use ATG as its start codon, ND2 and ND3 begin with ATT, and ND5 begin with ATA. Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.

A phylogenetic tree showed that two sequences of N. hainanensis shared a common evolutionary ancestry. Within subfamily Galericinae, H. suillus and the common ancestors of N. hainanensis and N. sinensis formed sister groups ( Figure 1). The results were consistent with morphological studies (Cobert 1988; Gould 1995; Grenyer and Purvis 2003). Our results support current taxonomy that places the N. hainanensis, N. sinensis and H. suillus in different genera (Smith et al. 2009; Wei et al. 2021). This mitochondrial genome sequence determined in this study will benefit future research into conservation genetics and phylogenetics for the species.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method.

Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

Ethical statement

This work complies with the International Union for Conservation of Nature (IUCN) policies research involving species at risk of extinction (see Guidelines for appropriate uses of IUCN Red list data version 4.0; https://www.iucnredlist.org/resources/guidelines-for-appropriate-uses-of-red-list-data ), as the species under study is an endangered species. All procedures were approved by Animal Research Ethics Committee of Hainan Provincial Education Center for Ecology and Environment, Hainan Normal University (HNECEE-2022-003) on March 6, 2022.

Data availability

Underlying data

NCBI Nucleotide: Neohylomys hainanensis voucher HN20N051 mitochondrion, complete genome. Accession number ON054206.2, https://www.ncbi.nlm.nih.gov/nuccore/ON054206.2 (Tu and Hou 2022).

Extended data

Figshare: Neohylomys hainanensis primer combinations data. https://doi.org/10.6084/m9.figshare.22180219.v1 (Tu 2023).

This project contains the following extended data:

- Primer information

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

References

Abramov AV, Bannikova AA, Lebedev VS, et al.: A broadly distributed species instead of an insular endemic? A new find of the poorly known Hainan gymnure (Mammalia, Lipotyphla). ZooKeys. 2018; 795: 77–81. Publisher Full Text
Cobert GB: The family Erinaceidae: a synthesis of its taxonomy, phylogeny, ecology and zoogeography. Mammal Rev. 1988; 18(3): 117–172.
Gould GC: Hedgehog phylogeny (Mammalia, Erinaceidae): The reciprocal illumination of the quick and the dead. Am. Mus. Novit. 1995; 1–45.
Grenyer R, Purvis A: A composite species-level phylogeny of the ‘Insectivora’ (Mammalia: Order Lipotyphla Haeckel,1866). J. Zool. 2003; 260: 245–257. Publisher Full Text
He K, Chen JH, Gould GC, et al.: An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach. PLoS One. 2012; 7(6): e39304. PubMed Abstract | Publisher Full Text | Free Full Text
Kumazawa Y: Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations. Gene. 2007; 388: 19–26. PubMed Abstract | Publisher Full Text
Liu SY, Wu Y: Handbook of the mammals of China. Fuzhou: The Strait Publishing & Distributing Group; 2019.
Lowe TM, Chan PP: tRNAscan-SE On-line: search and contextual analysis of transfer RNA genes. Nucleic Acids Res. 2016; 44(W1): W54–W57. PubMed Abstract | Publisher Full Text | Free Full Text
Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: a Laboratory Manual. (2nd ed). New York: Cold Spring Harbor Laboratory Press; 1989.
Shaw ZH, Wang S, Lu CK, et al.: A survey of the mammals of Hainan Island, China. Acta Zootaxonomica Sinica. 1966; 3(3): 260–276. Publisher Full Text
Shen YY, Liang L, Sun YB, et al.: A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol. Biol. 2010; 10: 132. PubMed Abstract | Publisher Full Text | Free Full Text
Smith AT, Xie Y, Wang S: A Guide to the Mammals of China. Changsha: Hunan Education Press; 2009.
Swindell SR, Plasterer TN: SEQMAN. Sequence Data Analysis Guidebook. New York: Springer; 1997.
Tamura K, Stecher G, Peterson D, et al.: MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 2013; 30: 2725–2729. PubMed Abstract | Publisher Full Text | Free Full Text
Tu F: Primer information.docx. Dataset. figshare. 2023. Publisher Full Text
Tu F, Hou X: Neohylomys hainanensis voucher HN20N051 mitochondrion, complete genome. [Dataset]. NCBI GenBank. 2022. Reference Source
Wei FW, Yang QS, Wu Y, et al.: Catalogue of mammals in China. Acta Theriologica Sinica. 2021; 41(5): 487–501.
Yue H, Yan CC, Tu FY, et al.: Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes. Biochem. Syst. Ecol. 2015; 60: 123–130. Publisher Full Text

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Version 2

VERSION 2 PUBLISHED 16 Mar 2023

Author details Author details

Feiyun Tu
Roles: Conceptualization, Formal Analysis, Funding Acquisition, Resources, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing

Xiaodan Hou
Roles: Investigation, Methodology, Software, Validation, Visualization

Qiujie Lu
Roles: Methodology, Software

Xiaofei Zhai
Roles: Data Curation, Investigation

Competing interests

No competing interests were disclosed.

Grant information

The study was supported by the project of the Natural Science Foundation of Hainan Province [No. 321RC544].
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Article Versions (2)

version 2

Revised

Published: 20 Oct 2025, 12:294

https://doi.org/10.12688/f1000research.131600.2

version 1

Published: 16 Mar 2023, 12:294

https://doi.org/10.12688/f1000research.131600.1

© 2025 Tu F et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Tu F, Hou X, Lu Q and Zhai X. The complete mitochondrial genome Hainan Gymnure, Neohylomys hainanensis [version 2; peer review: 2 approved with reservations]. F1000Research 2025, 12:294 (https://doi.org/10.12688/f1000research.131600.2)

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Open Peer Review

Version 1

VERSION 1

PUBLISHED 16 Mar 2023

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Reviewer Report 11 May 2024

Perinçek Seçkinozan Şeker, Artvin Çoruh University, Artvin, Turkey

Approved with Reservations

https://doi.org/10.5256/f1000research.144457.r250944

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Are the rationale for sequencing the genome and the species significance clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository?

Yes

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Molecular Systematics Zoology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Author Response 15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

15 Oct 2025

Author Response

Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm ... Continue reading Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Respond: We have revised the manuscript. We have compared the complete mitochondrial genome of Neohylomys hainanensis and previous reported genome sequence.
Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1,334bp).
Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Respond: We have revised the manuscript. We have compared the complete mitochondrial genome of Neohylomys hainanensis and previous reported genome sequence.
Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1,334bp).
Competing Interests: I am a author of this article. Close
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COMMENTS ON THIS REPORT

Author Response 15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

15 Oct 2025

Author Response

Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm ... Continue reading Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Respond: We have revised the manuscript. We have compared the complete mitochondrial genome of Neohylomys hainanensis and previous reported genome sequence.
Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1,334bp).
Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Respond: We have revised the manuscript. We have compared the complete mitochondrial genome of Neohylomys hainanensis and previous reported genome sequence.
Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1,334bp).
Competing Interests: I am a author of this article. Close
Report a concern

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Reviewer Report 04 Apr 2024

Michael Allen, Rutgers University, New Brunswick, USA

Approved with Reservations

https://doi.org/10.5256/f1000research.144457.r255823

General comments

This is a useful study in that it provides new genetic information for a poorly studied endangered species, the mammal Neohylomys hainanensis. The mitochondrial genome described therein will prove useful for future phylogenetic research as well as for metabarcoding studies of distribution and habitat use. While there was already a single complete genome for the species available in GenBank, the new genome and additional analysis provided by the authors provides novel information regarding intra- and inter-specific variation within the species and clade. The value of the paper could be enhanced to the extent that the authors can expand and elaborate on these analyses.

Detailed comments

TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.

Please state how many species are currently recognized within the family Erinaceidae.

Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.

Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.

Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?

Methods paragraph 3: “MEGA6.0” should have a space in it.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).

DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.

FIGURES

Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).

TABLES

While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.

Are the rationale for sequencing the genome and the species significance clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others?

Partly
Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository?

Yes

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Conservation, Environmental DNA, DNA metabarcoding, Bioinformatics

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Author Response 15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

15 Oct 2025

Author Response

TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title ... Continue reading TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title as: The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

Respond: We would like to provided full binomial name in the abstract.

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N. hainanensis is closely related to N. sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.
Respond: I agree with the revision.
Please state how many species are currently recognized within the family Erinaceidae.
Respond: In China, nine species are currently recognized within the family Erinaceidae.
Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.
Respond: We would like to delete the words “high level” in the revised manuscript.
Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”
Respond: I agree with the revision.

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.
Respond: I agree with the revision. Please change “…in the euthanasia cage (10L)…” into “…in a 10 L euthanasia cage…”.
Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.
Respond: Thank you for your suggestions. I agree with the revision.

A muscle sample was obtained from the preserved specimen, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989).

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?
Respond: We have changed as: “The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files”.
Methods paragraph 3: “MEGA6.0” should have a space in it.
Respond: Thank you for your suggestions. I agree with the revision.
To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA 6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.
Respond: We have provided Table 1.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”
Respond: Thank you for your suggestions. I agree with the revision.

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”
Respond: Thank you for your suggestions. I agree with the revision.

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).
Respond: Thank you for your suggestions.
DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.
Respond: Discussion section is not permitted by the journal.

FIGURES
Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).
Respond: Thank you for your suggestions.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method. Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

TABLES
While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.
Respond: Thank you for your suggestions.We have provided Table 1.
TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title as: The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

Respond: We would like to provided full binomial name in the abstract.

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N. hainanensis is closely related to N. sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.
Respond: I agree with the revision.
Please state how many species are currently recognized within the family Erinaceidae.
Respond: In China, nine species are currently recognized within the family Erinaceidae.
Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.
Respond: We would like to delete the words “high level” in the revised manuscript.
Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”
Respond: I agree with the revision.

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.
Respond: I agree with the revision. Please change “…in the euthanasia cage (10L)…” into “…in a 10 L euthanasia cage…”.
Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.
Respond: Thank you for your suggestions. I agree with the revision.

A muscle sample was obtained from the preserved specimen, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989).

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?
Respond: We have changed as: “The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files”.
Methods paragraph 3: “MEGA6.0” should have a space in it.
Respond: Thank you for your suggestions. I agree with the revision.
To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA 6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.
Respond: We have provided Table 1.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”
Respond: Thank you for your suggestions. I agree with the revision.

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”
Respond: Thank you for your suggestions. I agree with the revision.

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).
Respond: Thank you for your suggestions.
DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.
Respond: Discussion section is not permitted by the journal.

FIGURES
Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).
Respond: Thank you for your suggestions.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method. Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

TABLES
While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.
Respond: Thank you for your suggestions.We have provided Table 1.
Competing Interests: I am an AUTHOR of this article. Close
Report a concern
Respond or Comment

COMMENTS ON THIS REPORT

Author Response 15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

15 Oct 2025

Author Response

TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title ... Continue reading TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title as: The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

Respond: We would like to provided full binomial name in the abstract.

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N. hainanensis is closely related to N. sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.
Respond: I agree with the revision.
Please state how many species are currently recognized within the family Erinaceidae.
Respond: In China, nine species are currently recognized within the family Erinaceidae.
Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.
Respond: We would like to delete the words “high level” in the revised manuscript.
Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”
Respond: I agree with the revision.

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.
Respond: I agree with the revision. Please change “…in the euthanasia cage (10L)…” into “…in a 10 L euthanasia cage…”.
Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.
Respond: Thank you for your suggestions. I agree with the revision.

A muscle sample was obtained from the preserved specimen, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989).

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?
Respond: We have changed as: “The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files”.
Methods paragraph 3: “MEGA6.0” should have a space in it.
Respond: Thank you for your suggestions. I agree with the revision.
To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA 6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.
Respond: We have provided Table 1.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”
Respond: Thank you for your suggestions. I agree with the revision.

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”
Respond: Thank you for your suggestions. I agree with the revision.

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).
Respond: Thank you for your suggestions.
DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.
Respond: Discussion section is not permitted by the journal.

FIGURES
Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).
Respond: Thank you for your suggestions.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method. Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

TABLES
While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.
Respond: Thank you for your suggestions.We have provided Table 1.
TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title as: The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

Respond: We would like to provided full binomial name in the abstract.

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N. hainanensis is closely related to N. sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.
Respond: I agree with the revision.
Please state how many species are currently recognized within the family Erinaceidae.
Respond: In China, nine species are currently recognized within the family Erinaceidae.
Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.
Respond: We would like to delete the words “high level” in the revised manuscript.
Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”
Respond: I agree with the revision.

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.
Respond: I agree with the revision. Please change “…in the euthanasia cage (10L)…” into “…in a 10 L euthanasia cage…”.
Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.
Respond: Thank you for your suggestions. I agree with the revision.

A muscle sample was obtained from the preserved specimen, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989).

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?
Respond: We have changed as: “The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files”.
Methods paragraph 3: “MEGA6.0” should have a space in it.
Respond: Thank you for your suggestions. I agree with the revision.
To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA 6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.
Respond: We have provided Table 1.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”
Respond: Thank you for your suggestions. I agree with the revision.

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”
Respond: Thank you for your suggestions. I agree with the revision.

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).
Respond: Thank you for your suggestions.
DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.
Respond: Discussion section is not permitted by the journal.

FIGURES
Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).
Respond: Thank you for your suggestions.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method. Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

TABLES
While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.
Respond: Thank you for your suggestions.We have provided Table 1.
Competing Interests: I am an AUTHOR of this article. Close
Report a concern

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Version 2

VERSION 2 PUBLISHED 16 Mar 2023

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	1	2
Version 2 (revision) 20 Oct 25
Version 1 16 Mar 23	read	read

Michael Allen, Rutgers University, New Brunswick, USA
Perinçek Seçkinozan Şeker, Artvin Çoruh University, Artvin, Turkey

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Reviewer Report

14 Views

11 May 2024 | for Version 1

Perinçek Seçkinozan Şeker, Artvin Çoruh University, Artvin, Turkey

14 Views Cite this report Responses(1)

Approved With Reservations

Are the rationale for sequencing the genome and the species significance clearly described?

Partly
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others?

Yes
Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository?

Yes

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Molecular Systematics Zoology

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Author Response

15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

Thank you for your suggestions.

The authors report the complete mitochondrial DNA sequence of an insectivorous mammal species whose complete mitochondrial genome is already available at NCBI to confirm the accuracy of the data https://www.ncbi.nlm.nih.gov/nuccore/MW429379. At this point, the logic of sequencing the genome of this species and the importance of the species, which are the main issues that will emphasize the importance of the article, have not been sufficiently justified. Although this is even a genome announcement, this section should be developed by clearly stating the rationales. The methods used are up-to-date and fit for the study. The obtained genome sequence has been presented in a usable and accessible format in NCBI. A previously reported genome sequence of this species is available at NCBI. Therefore, it would be better to give the results of statistical analyses (for example, the topology of the phylogenetic tree and K2P distances) and the structures of the genomes comparatively. For example, there is a difference in length between the two genomes Why does this situation occur? It should be presented by comparing. As a result, this study presented as a genome note can be indexed if these requirements are improved.

Respond: We have revised the manuscript. We have compared the complete mitochondrial genome of Neohylomys hainanensis and previous reported genome sequence.
Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species, these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1,334bp).

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Competing Interests

I am a author of this article.

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Reviewer Report

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04 Apr 2024 | for Version 1

Michael Allen, Rutgers University, New Brunswick, USA

10 Views Cite this report Responses(1)

Approved With Reservations

Are the rationale for sequencing the genome and the species significance clearly described?

Yes
Are the protocols appropriate and is the work technically sound?

Yes
Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others?

Partly
Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository?

Yes

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Conservation, Environmental DNA, DNA metabarcoding, Bioinformatics

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Responses (1)

Author Response

15 Oct 2025

Feiyun Tu, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China

TITLE

Suggest changing the title to the following to improve clarity: “The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis”

Respond: We would like to change the title as: The complete mitochondrial genome of the Hainan Gymnure, Neohylomys hainanensis

ABSTRACT

“…the hainanensis, sinensis and suillus…”: These three species should be identified by their full binomial name here, not just the specific epithet. E.g., “N. hainanensis, Hylomys suillus and Neotetracus sinensis”

It would be good to report more detail here about what type of phylogenetic analysis was performed, if possible.

Respond: We would like to provided full binomial name in the abstract.

The Hainan Gymnure Neohylomys hainanensis is a small-size mammal which occurs in Hainan, China and north Vietnam. Here, we report the complete mitochondrial genome of N. hainanensis. The whole mitochondrial genome is 17,337 bp, and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and one control region. The base composition of the N. hainanensis total mitogenome is: 33.4% A, 12.2% G, 33.1% T, and C 21.3%, with an A + T content of 66.5%. The K2P genetic distance analysis supports current taxonomy that places N. hainanensis, Hylomys suillus and Neotetracus sinensis in different genera. Phylogenetic analysis suggests that N. hainanensis is closely related to N. sinensis based on the complete mitochondrial genome sequences. The mitogenomic data will contribute to molecular phylogenetics and conservation genetics of the species.

INTRODUCTION

Paragraph 1, sentences 1 & 2: Suggest rephrasing as follows: “The Hainan Gymnure (Neohylomys hainanensis Shaw and Wang, 1959) is a rodent distributed in Hainan, China and north Vietnam, where it inhabits tropical and subtropical forests (Smith et al. 2009; Liu and Wu 2019; Abramov et al. 2018).” I believe this would improve the flow and would serve to inform the reader what type of organism it is (i.e., a Mammal and a Rodent), information which is not currently provided.
Respond: I agree with the revision.
Please state how many species are currently recognized within the family Erinaceidae.
Respond: In China, nine species are currently recognized within the family Erinaceidae.
Paragraph 1, sentence 6: suggest deleting the words “high level” as their meaning is unclear here.
Respond: We would like to delete the words “high level” in the revised manuscript.
Paragraph 1, sentence 8: suggest changing “…to solve the disputes.” to “…in an attempt to resolve the current phylogenetic disputes.”
Respond: I agree with the revision.

METHODS

Methods paragraph 1, sentence 2: I recommend changing “…in the euthanasia cage (10L)…” to “…in a 10 L euthanasia cage…”. And, if possible, describe the cage and its material as the phrase “euthanasia cage” is not self-evident.
Respond: I agree with the revision. Please change “…in the euthanasia cage (10L)…” into “…in a 10 L euthanasia cage…”.
Methods paragraph 2, sentence 1: delete the word “the” from the phrase “using the phenol–chloroform extraction”.
Respond: Thank you for your suggestions. I agree with the revision.

A muscle sample was obtained from the preserved specimen, and the total genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol (Sambrook et al. 1989).

Methods paragraph 2, “All sequences were assembled and edited using SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997).”: Surely there must be more methods to report here in addition to which software you used. Are there any more details about settings used, etc., you can provide that would help someone better understand and repeat this analysis?
Respond: We have changed as: “The complete mitochondrial genome sequence was then assembled and manually refined utilizing SeqMan (DNASTAR 7.1.0) (Swindell and Plasterer 1997) following analysis of chromatogram files”.
Methods paragraph 3: “MEGA6.0” should have a space in it.
Respond: Thank you for your suggestions. I agree with the revision.
To better understand the phylogentic position of N. hainanensis within Eulipotyphla, we constructed a phylogenetic tree by using neighbor-joining (NJ) method implemented in MEGA 6.0 (Tamura et al. 2013) based on 13 complete mitochondrial genome sequences of Eulipotyphla using Kimura 2-parameters (K2P) model.

Methods paragraph 3 (“13 complete mitochondrial genome sequences of Eulipotyphla”): Please either state which species genomes were used here, or else reference Table 1 which I think provides that information. Also, please address why are there only 11 genomes displayed in Table 1 given that you analyzed 13. It would also be good to report how many species and genera are currently known to occur within Eulipotyphla. That would provide readers a better understanding of how complete your analysis is.
Respond: We have provided Table 1.

RESULTS

Results paragraph 1, sentence 4: sentence is incomplete as written. Please change to “Comparison with a previously published mitochondrial genome sequence (MW429379) for the same species revealed that these two sequences differ in length (17,337 bp vs 16,795 bp), which may be due to mitochondrial control region sequence variations (1,868 bp vs 1334bp).”
Respond: Thank you for your suggestions. I agree with the revision.

Results paragraph 1, penultimate sentence: Contains minor punctuation and wording issues. Rephrase as follows: “Most mitochondrial PCGs contain ATG as the start codon, ND2 and ND3 begin with ATT, and ND5 begins with ATA.”
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 2: The word “shaped” should be replaced with the word “formed” to improve clarity.
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, sentence 4: Please include the genus names or initials for these specific epithets. (See comment in Abstract.)
Thank you for your suggestions. I agree with the revision.

Results paragraph 2, last sentence: Change ending of sentence as follows to improve clarity: “…will benefit future research into conservation genetics and phylogenetics for the species.”
Respond: Thank you for your suggestions. I agree with the revision.

It would be useful to include summary statistics regarding pairwise K2P differences for different regions (e.g., in the context of DNA barcoding and metabarcoding).
Respond: Thank you for your suggestions.
DISCUSSION

Consider including a brief Discussion section if permitted by the journal format.
Respond: Discussion section is not permitted by the journal.

FIGURES
Figure 1: Please include in the caption the fact that this represents 10 species from the Eulipotyphla clade. Also, briefly explain that they were created using a neighbor-joining tree and that the codes after the species names represent GenBank accession numbers (if true).
Respond: Thank you for your suggestions.

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method. Nodal support indicated by bootstrap. The codes after the species names represent GenBank accession numbers.

TABLES
While not required, a table comparing the various attributes of the 2 known genomes of N. hainanensis (and perhaps other species analyzed) would be welcome.
Respond: Thank you for your suggestions.We have provided Table 1.

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Competing Interests

I am an AUTHOR of this article.

Alongside their report, reviewers assign a status to the article:

Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions

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The complete mitochondrial genome Hainan Gymnure, Neohylomys hainanensis

Abstract

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Methods

Results

Figure 1. A phylogenetic tree of ten species based on the complete mitochondrial genomes using NJ method.

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