The first mitochondrial genome of Haemagogus equinus from Jamaica

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Sandiford" }, { "@type": "Person", "name": "Simmoy A. A. Noble" }, { "@type": "Person", "name": "Samra A. Pierre" }, { "@type": "Person", "name": "Douglas E. Norris" }, { "@type": "Person", "name": "Renee Ali" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": "In the Americas, the expansion in incidence of arboviral infections including Mayaro virus (MAYV) has drawn attention to the resurgence of viruses associated with understudied arthropods. Mosquitoes belonging to the genus Haemagogus are generally geographically restricted to the forests of Central and South America and the Caribbean and are the known sylvan vectors for yellow fever virus and emerging MAYV. With an established population in Jamaica, Haemagogus equinus has been reported to be well-adapted to oviposition in artificial containers close to human populations. Its role in arboviral transmission however is not fully understood. Given the dearth of genetic information and the difficulty in morphologically identifying cryptic features in species belonging to this genus, we report the first mitochondrial genome of Hg. equinus. Using a genome skimming approach, two Hg. equinus mosquito specimens were sequenced using the Illumina Novaseq 6000 platform. A representative mitogenome of 16,471 bp, 80.7% AT and 37 genes was assembled using NOVOplasty. Phylogenetic analysis placed Hg. equinus in the Albomaculatus section of the Haemagogus subgenus supporting previously described taxonomic studies." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/13-1504/v1", "name": "The first mitochondrial genome of Haemagogus equinus from Jamaica" } } ] } Home Browse The first mitochondrial genome of Haemagogus equinus from Jamaica ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Sandiford SL, Noble SAA, Pierre SA et al. The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.12688/f1000research.159115.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] Simone L. Sandiford https://orcid.org/0000-0003-2368-0902 1,2 , Simmoy A. A. Noble 3 , Samra A. Pierre 4 , Douglas E. Norris https://orcid.org/0000-0002-4631-2777 5 , Renee Ali https://orcid.org/0009-0005-8050-9409 5 Simone L. Sandiford https://orcid.org/0000-0003-2368-0902 1,2 , Simmoy A. A. Noble 3 , [...] Samra A. Pierre 4 , Douglas E. Norris https://orcid.org/0000-0002-4631-2777 5 , Renee Ali https://orcid.org/0009-0005-8050-9409 5 PUBLISHED 09 Dec 2024 Author details Author details 1 Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 2 Mosquito Control and Research Unit, The University of the West Indies, Mona, Kingston, Jamaica 3 Department of Microbiology, Faculty of Medical Sciences, The University of the West Indies Mona, Kingston, Jamaica 4 Department of Life Sciences, Faculty of Science & Technology, The University of the West Indies Mona, Kingston, Jamaica 5 The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA Simone L. Sandiford Roles: Conceptualization, Project Administration, Resources, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Simmoy A. A. Noble Roles: Investigation, Resources, Writing – Review & Editing Samra A. Pierre Roles: Investigation, Resources, Writing – Review & Editing Douglas E. Norris Roles: Funding Acquisition, Resources, Writing – Review & Editing Renee Ali Roles: Data Curation, Formal Analysis, Methodology, Resources, Visualization, Writing – Original Draft Preparation OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Genomics and Genetics gateway. Abstract In the Americas, the expansion in incidence of arboviral infections including Mayaro virus (MAYV) has drawn attention to the resurgence of viruses associated with understudied arthropods. Mosquitoes belonging to the genus Haemagogus are generally geographically restricted to the forests of Central and South America and the Caribbean and are the known sylvan vectors for yellow fever virus and emerging MAYV. With an established population in Jamaica, Haemagogus equinus has been reported to be well-adapted to oviposition in artificial containers close to human populations. Its role in arboviral transmission however is not fully understood. Given the dearth of genetic information and the difficulty in morphologically identifying cryptic features in species belonging to this genus, we report the first mitochondrial genome of Hg. equinus. Using a genome skimming approach, two Hg. equinus mosquito specimens were sequenced using the Illumina Novaseq 6000 platform. A representative mitogenome of 16,471 bp, 80.7% AT and 37 genes was assembled using NOVOplasty. Phylogenetic analysis placed Hg. equinus in the Albomaculatus section of the Haemagogus subgenus supporting previously described taxonomic studies. READ ALL READ LESS Keywords Haemagogus equinus, mitogenome, Jamaica, arboviruses, genome skimming Corresponding Author(s) Simone L. Sandiford ( [email protected] ) Close Corresponding author: Simone L. Sandiford Competing interests: No competing interests were disclosed. Grant information: SAAN was supported in part by the University at Buffalo Clinical and Translational Science Institute award UL1TR001412 and the Global Infectious Diseases Research Training Program award D43TW010919. DEN and RA were supported in part by funding from the NSF-Accelerator Project D-688: Computing the Biome (2134862), Johns Hopkins Malaria Research Institute and Bloomberg Philanthropies. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2024 Sandiford SL 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: Sandiford SL, Noble SAA, Pierre SA et al. The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.12688/f1000research.159115.1 ) First published: 09 Dec 2024, 13 :1504 ( https://doi.org/10.12688/f1000research.159115.1 ) Latest published: 02 Jul 2025, 13 :1504 ( https://doi.org/10.12688/f1000research.159115.2 )  There is a newer version of this article available. Suppress this message for one day. Introduction Mosquitoes of the genus Haemagogus (Hg.) Williston, 1896 are endemic to tropical rainforests, open deciduous forests and mangroves in Latin America and the Caribbean. 1 The genus is divided into two subgenera ( Haemagogus and Conopostegus ), with the Haemagogus subgenus split into three sections (Albomaculatus, Splendens, Tropicalis). 1 Being the primary sylvatic vectors for yellow fever virus (YFV) 1 and the emerging arboviral threat Mayaro virus (MAYV), 2 species in this genus of mosquitoes are of significant medical importance in the region. Despite this, many species remain understudied and their role in disease transmission has not been clearly defined. In Jamaica, Haemagogus equinus Theobald, 1903 is presently the only known species on the island. Established populations of Hg. equinus have also been identified in southern Texas in the United States of America, Mexico, Belize, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Panama, Colombia, Guyana, Venezuela and Trinidad and Tobago. 1 While the vectorial capacity of Hg. equinus has not been fully elucidated, laboratory and transovarial transmission of YFV 3 – 6 along with natural infections among wild mosquitoes have been reported. 7 , 8 In spite of this, its importance in arboviral transmission in some localities remains uncertain. 9 Although Hg. equinus primarily oviposits and larvae develop in tree holes and bamboo internodes, 1 the species is very adaptable and can also utilize rock holes, 10 domestic containers and used tires. 11 , 12 With multiple reports of MAYV in neighbouring Haiti, 13 – 15 there is need for a greater understanding of the role of this sylvatic vector in arbovirus transmission. To facilitate this, accurate identification of all life stages of field collected specimens is crucial. However, impediments such as a lack of taxonomic expertise coupled with poor quality samples and a paucity of reference molecular data continue to hamper these efforts in Jamaica. Few studies have employed genomic sequencing to investigate the molecular taxonomy and phylogenetic relationships of Hg. equinus mosquitoes. Currently, only partial sequences of cytochrome oxidase I and other mitochondrial or nuclear genes are available from NCBI’s GenBank or BOLD systems databases. 16 – 21 The complete mitochondrial genome (mitogenome) is increasingly being used for evolutionary and phylogeny studies due to its maternal inheritance, simple genomic organization, relative abundance in tissues and absence of recombination. 22 In most metazoans the mitogenome is highly conserved and comprises of 13 protein coding genes, 22 transfer RNAs and two ribosomal RNAs in addition to a large single non-coding region important for replication and transcription. 23 At present, mitogenomes of only five species from the genus Haemagogus are available. 24 , 25 Considering the significance of mitogenomes when conducting phylogenetic and taxonomic studies, we describe for the first time the characterization of the mitogenome of Hg. equinus using a genome skimming approach and the phylogenetic comparison with other Haemagogus taxa. Methods The Hg. equinus samples (n = 2) sequenced were collected in Mona, Jamaica (18.0061364°N, -76.7515125°W) in May and December 2023 in an area characterized by the predominant growth of banana plants and adjacent to a forested area. Briefly, BG sentinel traps (BioGents, Regensburg, Germany) baited with two pounds of dry ice (without lure) were placed overnight from 1400 to 1000 hr and collected mosquito specimens were sorted and morphologically identified using taxonomic keys. 26 Single specimens were stored in tubes containing silica and shipped to the Johns Hopkins Bloomberg School of Public Health for molecular analysis as described in. 27 The mitogenome was assembled as described for African anophelines using NOVOPlasty (RRID:SCR_017335) version 4.3.1 27 , 28 and automatic annotations performed with MITOS on the galaxy platform under the invertebrate genetic code. 29 , 30 Geneious Prime (RRID:SCR_010519) version 2023.2.1 (Biomatters, Auckland, Australia) was utilized for manual adjustments of start and stop codons to match reference Haemagogus mitogenomes in the GenBank repository. Figure 1 illustrates a representative map of the mitochondrial sequences and annotations submitted to GenBank. Figure 1. Mitogenome map of Hg. equinus with annotated genes. Nine mitogenomes (two sequenced from this study and seven available from GenBank) were used for analysis. The 13 protein coding genes of these mitogenomes were extracted with Geneious Prime and aligned by MAFFT version 7.490 into a single matrix. jModelTest version 2.1.10 identified the best fit substitution model and phylogenetic analyses were performed using maximum likelihood in MEGA (RRID_SCR_023017) version 11 with 1000 bootstrap replicates. Results Sequencing of the two Hg. equinus specimens resulted in a mean of 26,728,491 million reads and of these approximately 69,261 reads were utilized for assembling each mitogenome. Two ribosomal RNAs, 22 transfer RNAs and 13 protein coding genes were detected in the two Hg. equinus mitochondrial genomes (GenBank accession numbers PQ_189398, PQ_189399). The cytochrome c oxidase I (COI) segment covering 1691-3221 bp was 99.59 % comparable to a COI sequence for Haemagogus spegazzinii Brèthes, 1912 (YP_010155459) retrieved from GenBank. Similar to the six Haemagogus mitochondrial genomes available in the GenBank database, the representative mitogenome from our sequencing efforts (PQ_189398) has an A+T proportion of 80.7% and length of 16,471 bp. The Maximum Likelihood phylogenetic tree places it in the Albomaculatus section, separated from other Haemagogus mitogenomes ( Figure 2 ). Figure 2. Maximum likelihood tree using the General Time Reversible (GTR + G + 1) substitution model based on the 13 concatanated protein coding genes of Hg. equinus , six Haemagogus species and Psorophora ferox von Humboldt, 1819 as an outgroup. These findings provide the basis for the development of more accurate molecular tools which can be used for identification of Hg. equinus mosquitoes. Furthermore, by populating molecular repositories with genomic data from Jamaican mosquitoes, their phylogenetic and evolutionary status will be better understood. Ethics and consent Ethical approval and consent were not required. Acknowledgments Simmoy A.A. Noble is a Global Infectious Diseases Scholar and received mentored research training in the development of this manuscript. Data availability GenBank: Haemagogus equinus mitochondrion, complete genome. Accession numbers PQ189398, PQ189399; https://identifiers.org/ncbi/insdc:PQ189398 , https://identifiers.org/ncbi/insdc:PQ189399 . 31 Bio Project. Complete mitochondrial genome of Haemagogus equinus , Accession number PRJNA1172362; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1172362 . 32 SRA. Illumina seq of Haemagogus equinus. Accession numbers SRR31002245, SRR31002246; https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA1172362 . 33 Biosample: Haemagogus equinus isolates HGJ1, HGJ3. SAMN44269491, SAMN44269492; https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1172362 . 34 References 1. Arnell JH: Mosquito studies (Diptera, Culicidae). XXXII. A revision of the genus Haemagogus. Contributions of the American Entomological Institute. 1973; 10 : ii + 1–ii + 174. 2. Pan American Health Organization: Epidemiological Alert: Mayaro Fever. (accessed on 15 August). Reference Source 3. Waddell MB, Taylor RM: Studies on Cyclic Passage of Yellow Fever Virus in South American Mammals and Mosquitoes: Marmosets (Callithrix aurita) and Cebus Monkeys (Cebus versutus) in Combination with Aedes aegypti and Haemagogus equinus. The American Journal of Tropical Medicine. 1945; s1-25 : 225–230. Publisher Full Text 4. Waddell MB, Taylor RM: Studies on the Cyclic Passage of Yellow Fever Virus in South American Mammals and Mosquitoes: III. Further Observations on Haemagogus equinus as a Vector of the Virus. The American Journal of Tropical Medicine. 1947; s1-27 : 471–476. Publisher Full Text 5. Waddell MB: Comparative Efficacy of Certain South American Aëdes and Haemagogus Mosquitoes as Laboratory Vectors of Yellow Fever. The American. J. Trop. Med. 1949; 29 : 567–575. PubMed Abstract | Publisher Full Text 6. Dutary BE, Leduc JW: Transovarial transmission of yellow fever virus by a sylvatic vector, Haemagogus equinus. Trans. R. Soc. Trop. Med. Hyg. 1981; 75 : 128. PubMed Abstract | Publisher Full Text 7. De Rodaniche E, Galindo P: Isolation of yellow fever virus from Haemagogus mesodentatus, H. equinus and Sabethes chloropterus captured in Guatemala in 1956. The American journal of tropical medicine and hygiene. 1957; 6 : 232–237. PubMed Abstract | Publisher Full Text 8. De Rodaniche E, Galindo P, Johnson CM: Isolation of yellow fever virus from Haemagogus lucifer, H. equinus, H. spegazzinii falco, Sabethes chloropterus and Anopheles neivai captured in Panama in the fall of 1956. The American journal of tropical medicine and hygiene. 1957; 6 : 681–685. 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Adeniran AA, Hernández-Triana LM, Ortega-Morales AI, et al. : Identification of mosquitoes (Diptera: Culicidae) from Mexico State, Mexico using morphology and COI DNA barcoding. Acta Trop. 2021; 213 : 105730. PubMed Abstract | Publisher Full Text 19. Viveros-Santos V, Hernández-Triana LM, Ibáñez-Bernal S, et al. : Integrated Approaches for the Identification of Mosquitoes (Diptera: Culicidae) from the Volcanoes of Central America Physiographic Subprovince of the State of Chiapas, Mexico. Vector borne and zoonotic diseases (Larchmont, N.Y.). 2022; 22 : 120–137. PubMed Abstract | Publisher Full Text 20. Hernández-Triana LM, Garza-Hernández JA, Ortega Morales AI, et al. : An Integrated Molecular Approach to Untangling Host–Vector–Pathogen Interactions in Mosquitoes (Diptera: Culicidae) From Sylvan Communities in Mexico. Front. Vet. Sci. 2021; 7 . PubMed Abstract | Publisher Full Text | Free Full Text 21. Reidenbach KR, Cook S, Bertone MA, et al. : Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology. BMC Evol. Biol. 2009; 9 : 298. PubMed Abstract | Publisher Full Text | Free Full Text 22. Cameron SL: Insect mitochondrial genomics: implications for evolution and phylogeny. Annu. Rev. Entomol. 2014; 59 : 95–117. Publisher Full Text 23. Boore JL: Animal mitochondrial genomes. Nucleic Acids Res. 1999; 27 : 1767–1780. PubMed Abstract | Publisher Full Text | Free Full Text 24. da Silva FS , Cruz ACR, de Almeida Medeiros DB , et al. : Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae). Sci. Rep. 2020; 10 : 16948. PubMed Abstract | Publisher Full Text | Free Full Text 25. Lemos PS, Monteiro HAO, Castro FC, et al. : Characterization of mitochondrial genome of Haemagogus janthinomys (Diptera: Culicidae). Mitochondrial DNA Part A. 2017; 28 : 50–51. PubMed Abstract | Publisher Full Text 26. Belkin JN, Heinemann SJ, Page WA: The Culicidae of Jamaica (Mosquito Studies. XXI). Contrib. Am. Entomol. Inst. 1970; 6 : 1–458. 27. Ali R, Gebhardt M, Lupiya J, et al. : The first complete mitochondrional genome of Anopheles gibbinsi using a skimming sequencing approach. [version 1; peer review: 3 approved]. F1000Res. 2024; 13 : 553. PubMed Abstract | Publisher Full Text | Free Full Text 28. Dierckxsens N, Mardulyn P, Smits G: NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017; 45 : e18. PubMed Abstract | Publisher Full Text | Free Full Text 29. Bernt M, Donath A, Jühling F, et al. : MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 2013; 69 : 313–319. PubMed Abstract | Publisher Full Text 30. Afgan E, Baker D, Batut B, et al. : The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018; 46 : W537–W544. PubMed Abstract | Publisher Full Text | Free Full Text 31. Noble SAA, Pierre SA, Sandiford SL, et al. : Haemagogus equinus mitochondrion, complete genome. [Dataset]. GenBank. 2024. 32. Johns Hopkins Bloomberg School of Public Health: Complete mitochondrial genome of Haemagogus equinus. [Dataset]. Bioproject. 2024. 33. Johns Hopkins Bloomberg School of Public Health: llumina seq of Haemagogus equinus. [Dataset]. SRA. 2024. 34. Johns Hopkins Bloomberg School of Public Health: Invertebrate sample of Haemagogus equinus. [Dataset]. Biosample. 2024. Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 09 Dec 2024 ADD YOUR COMMENT Comment Author details Author details 1 Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 2 Mosquito Control and Research Unit, The University of the West Indies, Mona, Kingston, Jamaica 3 Department of Microbiology, Faculty of Medical Sciences, The University of the West Indies Mona, Kingston, Jamaica 4 Department of Life Sciences, Faculty of Science & Technology, The University of the West Indies Mona, Kingston, Jamaica 5 The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA Simone L. Sandiford Roles: Conceptualization, Project Administration, Resources, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing Simmoy A. A. Noble Roles: Investigation, Resources, Writing – Review & Editing Samra A. Pierre Roles: Investigation, Resources, Writing – Review & Editing Douglas E. Norris Roles: Funding Acquisition, Resources, Writing – Review & Editing Renee Ali Roles: Data Curation, Formal Analysis, Methodology, Resources, Visualization, Writing – Original Draft Preparation Competing interests No competing interests were disclosed. Grant information SAAN was supported in part by the University at Buffalo Clinical and Translational Science Institute award UL1TR001412 and the Global Infectious Diseases Research Training Program award D43TW010919. DEN and RA were supported in part by funding from the NSF-Accelerator Project D-688: Computing the Biome (2134862), Johns Hopkins Malaria Research Institute and Bloomberg Philanthropies. 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: 02 Jul 2025, 13:1504 https://doi.org/10.12688/f1000research.159115.2 version 1 Published: 09 Dec 2024, 13:1504 https://doi.org/10.12688/f1000research.159115.1 Copyright © 2024 Sandiford SL 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. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Sandiford SL, Noble SAA, Pierre SA et al. The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.12688/f1000research.159115.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE 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 Version 1 VERSION 1 PUBLISHED 09 Dec 2024 Views 0 Cite How to cite this report: Wilding C. Reviewer Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349839 ) The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349839 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 29 Jan 2025 Craig Wilding , School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland Approved VIEWS 0 https://doi.org/10.5256/f1000research.174799.r349839 Sandiford et al sequence full mitochondrial genomes from genome skimming data from two Haemagogus equinus specimens collected from Jamaica. They assemble these into a full mtDNA genome containing the expected gene content. Their introduction is well-written and provides much background ... Continue reading READ ALL Sandiford et al sequence full mitochondrial genomes from genome skimming data from two Haemagogus equinus specimens collected from Jamaica. They assemble these into a full mtDNA genome containing the expected gene content. Their introduction is well-written and provides much background information and adequate justification for this study. However, I would argue that the statement in the introduction that “Few studies have employed genomic sequencing to investigate the molecular taxonomy and phylogenetic relationships of Hg. equinus mosquitoes” suggests that this paper is going to provide a genome. Whilst it could be argued that the mtDNA is a genome it is somewhat misleading! In the Methods there is no information on the sequencing undertaken. Whilst the authors say “molecular analysis as described in [27]” this is insufficient – at the very least there should be a brief description of what was done. The statement “Nine mitogenomes (two sequenced from this study and seven available from GenBank) were used for analysis” should read “Nine mitogenomes (two sequenced from this study and seven available from GenBank) were used for phylogenetic analysis” In the Results section, Figure 1 has a very poor resolution. This needs altering. Figure 2 has the albomaculatus and tropical groups highlighted, but which group does Hg. leucocelaenus belong? Is this Splendens? Or if not, are there no mitochondrial genomes from this group? I am not particularly clear on the point of Figure 2. It would make more sense to produce a tree on a wider-scale (including e.g. representative Aedes and Sabethes or, have a tree to show the reader the position of Hg. equinus within the wider Aedini and then have this zoomed in view of Haemagogus , but for those readers unfamiliar with this genus the Figure does not really say anything of use and the text merely says “The Maximum Likelihood phylogenetic tree places it in the Albomaculatus section”. Was this not known before these mitochondrial sequences were generated? The authors make no comment on whether the gene order seen in this species is as expected given those of closely related species. They should do so. This study sequenced two specimens with accession numbers PQ_189398 and PQ_189399. How different were they? Some indication of overall genetic distance would be useful. 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? No 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: Evolutionary genetics 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. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Wilding C. Reviewer Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349839 ) The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349839 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 11 Sep 2025 Simone Sandiford , Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 11 Sep 2025 Author Response Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular ... Continue reading Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular analysis to the methods section and stated the similarity between the 2 sequenced specimens in the results. Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular analysis to the methods section and stated the similarity between the 2 sequenced specimens in the results. Competing Interests: All authors declare no competing interest. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 11 Sep 2025 Simone Sandiford , Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 11 Sep 2025 Author Response Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular ... Continue reading Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular analysis to the methods section and stated the similarity between the 2 sequenced specimens in the results. Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular analysis to the methods section and stated the similarity between the 2 sequenced specimens in the results. Competing Interests: All authors declare no competing interest. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Syafruddin D and Setia Asih PB. Reviewer Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349846 ) The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349846 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 08 Jan 2025 Din Syafruddin , National Research and Innovation Agency (BRIN), Makassa, Indonesia Puji Budi Setia Asih , Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Indonesia, Indonesia Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.174799.r349846 General comment: The manuscript reports the complete mitochondrial genome sequence of Haemagogus equinus from Jamaica. The genome is circular and includes 13 protein-coding genes, 2 ribosomal RNA genes and 22 tRNA genes. As the member of tribe ... Continue reading READ ALL General comment: The manuscript reports the complete mitochondrial genome sequence of Haemagogus equinus from Jamaica. The genome is circular and includes 13 protein-coding genes, 2 ribosomal RNA genes and 22 tRNA genes. As the member of tribe Aedini and vector of Yellow fever, it might be informative to include mitochondrial genome of Aedes aegypti in the phylogenetic tree. Specific comments: The map should clearly indicate the position of the 13 protein coding genes, rRNA genes and 22 tRNA genes in the light and heavy strands of mtDNA (Fig. 1). The authors should include “discussion” section in the manuscript to describe the characteristic of the genes encode by mitochondrial gnome of the Haemogogus equinus in comparison to cosmopolitan species of the tribe Aedini, Aedes aegypti . 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? 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. We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Syafruddin D and Setia Asih PB. Reviewer Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349846 ) The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349846 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 02 Jul 2025 Simone Sandiford , Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 02 Jul 2025 Author Response Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and ... Continue reading Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and a detailed protocol in the methods section which discusses the sequencing of the genome. We have fulfilled both requirements. A results section is optional, and we have chosen to provide this also. A discussion section is not needed hence it was not included. As it relates to the tree, Psorophora ferox was used as an outgroup as it is also a member of tribe Aedini and like Haemagogus equinus , is a forest mosquito. Figure 1 was constructed similar to other illustrated figures in genome notes which have previously been published and unanimously approved by peer reviewers in F1000Research as indicated below. https://f1000research.com/articles/12-330 https://f1000research.com/articles/13-553 Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and a detailed protocol in the methods section which discusses the sequencing of the genome. We have fulfilled both requirements. A results section is optional, and we have chosen to provide this also. A discussion section is not needed hence it was not included. As it relates to the tree, Psorophora ferox was used as an outgroup as it is also a member of tribe Aedini and like Haemagogus equinus , is a forest mosquito. Figure 1 was constructed similar to other illustrated figures in genome notes which have previously been published and unanimously approved by peer reviewers in F1000Research as indicated below. https://f1000research.com/articles/12-330 https://f1000research.com/articles/13-553 Competing Interests: No competing interests Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 02 Jul 2025 Simone Sandiford , Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica 02 Jul 2025 Author Response Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and ... Continue reading Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and a detailed protocol in the methods section which discusses the sequencing of the genome. We have fulfilled both requirements. A results section is optional, and we have chosen to provide this also. A discussion section is not needed hence it was not included. As it relates to the tree, Psorophora ferox was used as an outgroup as it is also a member of tribe Aedini and like Haemagogus equinus , is a forest mosquito. Figure 1 was constructed similar to other illustrated figures in genome notes which have previously been published and unanimously approved by peer reviewers in F1000Research as indicated below. https://f1000research.com/articles/12-330 https://f1000research.com/articles/13-553 Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and a detailed protocol in the methods section which discusses the sequencing of the genome. We have fulfilled both requirements. A results section is optional, and we have chosen to provide this also. A discussion section is not needed hence it was not included. As it relates to the tree, Psorophora ferox was used as an outgroup as it is also a member of tribe Aedini and like Haemagogus equinus , is a forest mosquito. Figure 1 was constructed similar to other illustrated figures in genome notes which have previously been published and unanimously approved by peer reviewers in F1000Research as indicated below. https://f1000research.com/articles/12-330 https://f1000research.com/articles/13-553 Competing Interests: No competing interests Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 09 Dec 2024 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline 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 Reviewer Reports Invited Reviewers 1 2 3 Version 2 (revision) 02 Jul 25 read Version 1 09 Dec 24 read read Din Syafruddin , National Research and Innovation Agency (BRIN), Makassa, Indonesia Puji Budi Setia Asih , National Research and Innovation Agency, Indonesia, Indonesia Craig Wilding , University College Dublin, Dublin, Ireland Alexey Makunin , Wellcome Sanger Institute, Hinxton, UK Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Makunin A. This is an open access peer review report 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. 04 Nov 2025 | for Version 2 Alexey Makunin , Wellcome Sanger Institute, Hinxton, England, UK 0 Views copyright © 2025 Makunin A. This is an open access peer review report 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. format_quote Cite this report speaker_notes Responses (0) Approved info_outline 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 The manuscript by Sandiford, et al., describes two mitochondrial genomes for arboviral vector mosquito Haemagogus equinus . The dataset is succinctly described and characterised to ensure that the resulting mitochondrial genomes become a valuable resource for future studies. I only have several minor comments: - Illumina read length and layout (single or paired end) are not specified - "manual adjustments of start and stop codons to match reference _ Haemagogus _ mitogenomes in the GenBank repository" - if the sequencing effort did not allow to accurately reconstruct start and stop codon, the accuracy of the remaining sequence and subsequent phylogenetic analysis can be compromised - Selected optimal substitution model for phylogenetic analysis is not specified. Also, it seems that the entire matrix was treated as a single partition, without considering separate models for different codon positions - is it correct? - COI analysis looks a bit confusing - the coordinates are given for the entire gene, not the ~658bp fragment used for barcoding. "99.59 % comparable to a COI sequence for Haemagogus spegazzinii (YP_010155459)" seemingly indicates protein identity for 510aa segment in YP_010155459, which does not seem relevant for species identification. While this might be out of scope for this particular study (given the complete MT PCG tree looks convincing and Hg. equinus does not seem to be closely related to any other species with complete MT available), I would suggest building a tree based on nucleotide sequence of COI barcode for all Hg. records in BOLD with extracts from two new mitogenomes added - this would complement and verify the PCG tree results with more observations, but smaller resolution. 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? 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 Comparative genomics, chromosome evolution 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. reply Respond to this report Responses (0) Makunin A. Peer Review Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.184140.r421208) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/13-1504/v2#referee-response-421208 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Wilding C. This is an open access peer review report 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. 29 Jan 2025 | for Version 1 Craig Wilding , School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland 0 Views copyright © 2025 Wilding C. This is an open access peer review report 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. format_quote Cite this report speaker_notes Responses (1) Approved info_outline 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 Sandiford et al sequence full mitochondrial genomes from genome skimming data from two Haemagogus equinus specimens collected from Jamaica. They assemble these into a full mtDNA genome containing the expected gene content. Their introduction is well-written and provides much background information and adequate justification for this study. However, I would argue that the statement in the introduction that “Few studies have employed genomic sequencing to investigate the molecular taxonomy and phylogenetic relationships of Hg. equinus mosquitoes” suggests that this paper is going to provide a genome. Whilst it could be argued that the mtDNA is a genome it is somewhat misleading! In the Methods there is no information on the sequencing undertaken. Whilst the authors say “molecular analysis as described in [27]” this is insufficient – at the very least there should be a brief description of what was done. The statement “Nine mitogenomes (two sequenced from this study and seven available from GenBank) were used for analysis” should read “Nine mitogenomes (two sequenced from this study and seven available from GenBank) were used for phylogenetic analysis” In the Results section, Figure 1 has a very poor resolution. This needs altering. Figure 2 has the albomaculatus and tropical groups highlighted, but which group does Hg. leucocelaenus belong? Is this Splendens? Or if not, are there no mitochondrial genomes from this group? I am not particularly clear on the point of Figure 2. It would make more sense to produce a tree on a wider-scale (including e.g. representative Aedes and Sabethes or, have a tree to show the reader the position of Hg. equinus within the wider Aedini and then have this zoomed in view of Haemagogus , but for those readers unfamiliar with this genus the Figure does not really say anything of use and the text merely says “The Maximum Likelihood phylogenetic tree places it in the Albomaculatus section”. Was this not known before these mitochondrial sequences were generated? The authors make no comment on whether the gene order seen in this species is as expected given those of closely related species. They should do so. This study sequenced two specimens with accession numbers PQ_189398 and PQ_189399. How different were they? Some indication of overall genetic distance would be useful. 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? No 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 Evolutionary genetics 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. reply Respond to this report Responses (1) Author Response 11 Sep 2025 Simone Sandiford, Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica Thank you for your insightful comments regarding our manuscript. As suggested, we have replaced Figure 1 with a high quality version, enhanced Figure 2, added further details regarding the molecular analysis to the methods section and stated the similarity between the 2 sequenced specimens in the results. View more View less Competing Interests All authors declare no competing interest. reply Respond Report a concern Wilding C. Peer Review Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349839) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349839 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Syafruddin D et al. This is an open access peer review report 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. 08 Jan 2025 | for Version 1 Din Syafruddin , National Research and Innovation Agency (BRIN), Makassa, Indonesia Puji Budi Setia Asih , Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Indonesia, Indonesia 0 Views copyright © 2025 Syafruddin D et al. This is an open access peer review report 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. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline 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 General comment: The manuscript reports the complete mitochondrial genome sequence of Haemagogus equinus from Jamaica. The genome is circular and includes 13 protein-coding genes, 2 ribosomal RNA genes and 22 tRNA genes. As the member of tribe Aedini and vector of Yellow fever, it might be informative to include mitochondrial genome of Aedes aegypti in the phylogenetic tree. Specific comments: The map should clearly indicate the position of the 13 protein coding genes, rRNA genes and 22 tRNA genes in the light and heavy strands of mtDNA (Fig. 1). The authors should include “discussion” section in the manuscript to describe the characteristic of the genes encode by mitochondrial gnome of the Haemogogus equinus in comparison to cosmopolitan species of the tribe Aedini, Aedes aegypti . 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? 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. We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 02 Jul 2025 Simone Sandiford, Department of Basic Medical Sciences, Pharmacology and Pharmacy Section, Faculty of Medical Sciences,, The University of the West Indies Mona, Kingston, Jamaica Thank you to the reviewers for the feedback provided. Our article was submitted as a genome note. Based on the F1000Research guidelines genome notes only require an introduction and a detailed protocol in the methods section which discusses the sequencing of the genome. We have fulfilled both requirements. A results section is optional, and we have chosen to provide this also. A discussion section is not needed hence it was not included. As it relates to the tree, Psorophora ferox was used as an outgroup as it is also a member of tribe Aedini and like Haemagogus equinus , is a forest mosquito. Figure 1 was constructed similar to other illustrated figures in genome notes which have previously been published and unanimously approved by peer reviewers in F1000Research as indicated below. https://f1000research.com/articles/12-330 https://f1000research.com/articles/13-553 View more View less Competing Interests No competing interests reply Respond Report a concern Syafruddin D and Setia Asih PB. Peer Review Report For: The first mitochondrial genome of Haemagogus equinus from Jamaica [version 1; peer review: 1 approved, 1 approved with reservations] . F1000Research 2024, 13 :1504 ( https://doi.org/10.5256/f1000research.174799.r349846) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/13-1504/v1#referee-response-349846 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. 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