{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:49:56Z","timestamp":1792788596405,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/f1000research.179613.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000}}],"reference-count":26,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Direcci\u00f3n de Investigaci\u00f3n, Universidad Nacional de Colombia","id":[{"id":"https:\/\/ror.org\/059yx9a68","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    (\u201cbee-assassin\u201d assassin bugs) is a Neotropical genus of Reduviidae with ecological importance as a group of predatory insects and notable morphological diversity, yet mitochondrial genomic resources have remained unavailable for the genus. We generated low-coverage whole-genome sequencing data from four vouchered specimens collected in Colombia and reconstructed mitochondrial genomes for\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    sp.,\n                    <ns3:italic>A. ochropterus<\/ns3:italic>\n                    ,\n                    <ns3:italic>A. luctuosus<\/ns3:italic>\n                    , and\n                    <ns3:italic>A. nitidicollis<\/ns3:italic>\n                    . Quality-filtered reads were assembled using an organelle-specific GetOrganelle workflow, and the resulting assembly graphs and candidate sequences were evaluated against initial SPAdes\/BLASTN-based reconstructions. GetOrganelle recovered complete circular mitochondrial genomes for\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    sp.,\n                    <ns3:italic>A. ochropterus<\/ns3:italic>\n                    , and\n                    <ns3:italic>A. nitidicollis<\/ns3:italic>\n                    , whereas\n                    <ns3:italic>A. luctuosus<\/ns3:italic>\n                    was represented by a single gap-free, non-circularized mitochondrial scaffold in which the control region was not completely recovered. The selected assemblies ranged from 14,943 to 19,405 bp and were strongly AT-rich. Annotation and manual curation recovered the complete complement of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes in all four taxa. Comparative analysis showed complete conservation of mitochondrial gene content, gene order, and transcriptional orientation, with no evidence of gene rearrangements among the sampled species. Phylogenetic analysis based on concatenated mitochondrial protein-coding genes recovered the four\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    taxa as a monophyletic group, with\n                    <ns3:italic>A. ochropterus<\/ns3:italic>\n                    and\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    sp. forming a sister pair,\n                    <ns3:italic>A. nitidicollis<\/ns3:italic>\n                    sister to that clade, and\n                    <ns3:italic>A. luctuosus<\/ns3:italic>\n                    occupying the basal position among the sampled taxa. These assemblies constitute the first mitochondrial genomic resources for\n                    <ns3:italic>Apiomerus<\/ns3:italic>\n                    and expand the representation of Apiomerini for comparative mitogenomic, taxonomic, and phylogenetic studies.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.179613.2","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T07:44:06Z","timestamp":1787730246000},"page":"921","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Mitochondrial Genome Assemblies of Four \u201cBee-Assassin\u201d (Hemiptera: Reduviidae: Apiomerus) Recovered Using Shallow Whole-Genome sequencing"],"prefix":"10.12688","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1069-9199","authenticated-orcid":false,"given":"Andr\u00e9s","family":"G\u00f3mez-Palacio","sequence":"first","affiliation":[{"name":"Laboratorio de Investigaci\u00f3n en Gen\u00e9tica Evolutiva - LIGE. Tunja Boyaca Universidad Pedagogica y Tecnologica de Colombia"},{"name":"Grupo de Estudios en Gen\u00e9tica y Biolog\u00eda Molecular - GEBIMOL Tunja Boyac\u00e1 Universidad Pedag\u00f3gica y Tecnol\u00f3gica de Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Uribe-Soto","sequence":"additional","affiliation":[{"name":"Grupo de Investigaci\u00f3n en Sistem\u00e1tica Molecular - GSM Medell\u00edn Universidad Nacional de Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Ortiz-Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Grupo de Investigaci\u00f3n en Sistem\u00e1tica Molecular - GSM Medell\u00edn Universidad Nacional de Colombia"},{"name":"Centro de Investigaci\u00f3n La Selva, Corporaci\u00f3n Colombiana de Investigaci\u00f3n Agropecuaria Rionegro Antioquia AGROSAVIA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6358-757X","authenticated-orcid":false,"given":"Dimitri","family":"Forero","sequence":"additional","affiliation":[{"name":"Universidad Nacional de Colombia, sede Bogot\u00e1, Facultad de Ciencias Bogot\u00e1 Bogota National University of Colombia Natural Sciences Institute"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"ref1","first-page":"694","article-title":"Maldonado Capriles, J. 1990. Systematic Catalogue of the Reduviidae of the World (Insecta: Heteroptera).","volume":"51","author":"M Coscar\u00f3n","year":"2017 Apr","journal-title":"Edici\u00f3n especial del Caribbcan Journal of Science."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"283-302","DOI":"10.1016\/j.ympev.2012.10.002","article-title":"Phylogeny and character evolution in the bee-assassins (Insecta: Heteroptera: Reduviidae).","volume":"66","author":"D Forero","year":"2013 Jan","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"307-351","DOI":"10.1007\/978-94-017-9861-7_12","author":"H Gil-Santana","year":"2015 cited 2026 Feb 23","journal-title":"True Bugs (Heteroptera) of the Neotropics."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"57-68","DOI":"10.11646\/zootaxa.2331.1.3","article-title":"Taxonomical and biological notes on Neotropical Apiomerini (Hemiptera: Heteroptera: Reduviidae: Harpactorinae).","volume":"2331","author":"H Gil-Santana","year":"2010 Jan","journal-title":"Zootaxa."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"20171223","DOI":"10.1098\/rspb.2017.1223","article-title":"Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs.","volume":"284","author":"H Li","year":"2017 Sep 13","journal-title":"Proc. R. Soc. B."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"83-101","DOI":"10.1146\/annurev-ento-013024-015553","article-title":"Insect Mitochondrial Genomics: A Decade of Progress.","volume":"70","author":"S Cameron","year":"2025 Jan 28","journal-title":"Annu. Rev. Entomol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1767-1780","DOI":"10.1093\/nar\/27.8.1767","article-title":"Animal mitochondrial genomes.","volume":"27","author":"J Boore","year":"1999 Apr 1","journal-title":"Nucleic Acids Res."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"545-579","DOI":"10.1146\/annurev.ecolsys.37.091305.110018","article-title":"Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA.","volume":"37","author":"C Simon","year":"2006 Dec 1","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"3155-3156","DOI":"10.1080\/23802359.2019.1667272","article-title":"The mitochondrial genome of the assassin bug Sclomina erinacea (Hemiptera: Reduviidae).","volume":"4","author":"Q Zhao","year":"2019 Jul 3","journal-title":"Mitochondrial DNA Part B."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1183-1201","DOI":"10.1111\/1755-0998.12660","article-title":"Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.","volume":"17","author":"J Sproul","year":"2017 Nov","journal-title":"Mol. Ecol. Resour."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e96793","DOI":"10.1371\/journal.pone.0096793","article-title":"Sequencing Degraded DNA from Non-Destructively Sampled Museum Specimens for RAD-Tagging and Low-Coverage Shotgun Phylogenetics. Caramelli D, editor.","volume":"9","author":"M Tin","year":"2014 May 14","journal-title":"PLoS One."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"5-41","DOI":"10.1002\/mmnd.201200001","article-title":"Comparative genitalic morphology in the New World resin bugs Apiomerini (Hemiptera, Heteroptera, Reduviidae, Harpactorinae).","volume":"59","author":"D Forero","year":"2012","journal-title":"Deutsche Entomologische Zeitschrift."},{"key":"ref13","first-page":"213-218","article-title":"Notas sobre algumas esp\u00e9cies de \u201cApiomerus\u201d Hahn do Brasil (Heteroptera: Reduviidae: Harpactorinae: Apiomerini).","author":"H Gil-Santana","year":"2006 cited 2025 Nov 21","journal-title":"Bolet\u00edn de la SEA."},{"key":"ref14","first-page":"235-302","article-title":"Bidrag till Reduviidernas k\u00e4nnedom.","volume":"23","author":"S Carl","year":"1866","journal-title":"\u00d6fversigt af Kongl Vetenskaps-akademiens forhandlingar."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"938-1876","DOI":"10.5962\/bhl.title.12549","year":"1870","journal-title":"Enumeratio hemipterorum: bidrag till en f\u00f6rteckning \u00f6fver alla hittills k\u00e4nda hemiptera, jemte systematiska meddelanden. bd.1\u20135 (1870-1876)."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"i884-i890","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics.","volume":"34","author":"S Chen","year":"2018"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler.","author":"A Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinformatics."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1186\/s13059-020-02154-5","article-title":"GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.","volume":"21","author":"J Jin","year":"2020 Sep 10","journal-title":"Genome Biol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"3094-3100","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences.","volume":"34","author":"H Li","year":"2018 Sep 1","journal-title":"Bioinformatics."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools.","volume":"10","author":"P Danecek","year":"2021","journal-title":"Gigascience."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"10543-10552","DOI":"10.1093\/nar\/gkz833","article-title":"Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.","volume":"47","author":"A Donath","year":"2019 Nov 18","journal-title":"Nucleic Acids Res."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"9077-9096","DOI":"10.1093\/nar\/gkab688","article-title":"tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes.","volume":"49","author":"P Chan","year":"2021 Sep 20","journal-title":"Nucleic Acids Res."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"2811-2812","DOI":"10.1093\/bioinformatics\/btu393","article-title":"circlize implements and enhances circular visualization in R.","volume":"30","author":"Z Gu","year":"2014 Oct 1","journal-title":"Bioinformatics."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"3059-3066","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.","volume":"30","author":"K Katoh","year":"2002 Jul","journal-title":"Nucleic Acids Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"39-64","DOI":"10.1007\/978-1-59745-251-9_3","author":"K Katoh","year":"2009","journal-title":"Bioinformatics for DNA sequence analysis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1530-1534","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.","volume":"37","author":"B Minh","year":"2020 May","journal-title":"Mol. Biol. Evol."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/15-921\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-921\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-921\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T07:49:10Z","timestamp":1790668150000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/15-921\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,26]]},"references-count":26,"URL":"https:\/\/doi.org\/10.12688\/f1000research.179613.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/f1000research.179613.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.208114.r514759","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.208114.r522072","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.208114.r518524","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.208114.r514759","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.208114.r522072","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.208114.r518524","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,26]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.198144.r494385, Annabel Whibley, The University of Auckland, Auckland, Auckland, 08 Jul 2026, version 1, 3 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-921\/v1#referee-response-494385","order":0,"name":"referee-response-494385","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Andr&eacute;s G&oacute;mez-Palacio<\/b>; \n<i>Posted: 05 Aug 2026<\/i>; Dr. Annabel Whibley  \n<u><i>We sincerely thank you for the careful and constructive evaluation of our manuscript and for the helpful recommendations regarding its presentation and methodological clarity. Each comment and concern is addressed individually in the point-by-point responses below.<\/i><\/u>  G&oacute;mez-Palacio and colleagues report 4 complete mitochondrial genome assemblies of \u201cbee-killer\u201d assassin bugs. These assemblies were generated from vouchered specimens and low-coverage Illumina datasets. Contigs with homology to characterized mitogenomes were extracted from these assemblies and used to generate complete mitogenome representations, which were subsequently annotated. These assemblies show the expected complement of annotated genes, tRNA and rRNAs (with some ambiguity noted in one species). The assemblies are used to support a phylogenetic assessment, with additional species from public databases, The subdivision of the abstract into a background, methods and results section seems unusual- should this be written as a conventional narrative paragraph?  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for this suggestion. The abstract has been rewritten as a single narrative paragraph without section headings. We also revised the abstract and Methods to reflect the updated GetOrganelle-based assembly workflow and the conservative classification of the resulting mitochondrial assemblies.<\/i>  The paper is well written and methods are sound, with a good level of background information to provide context to the work.  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for this positive assessment of the manuscript and its methodological and contextual foundation.<\/i>  The one step that I feel is not well explained (and reason for the \u201cpartly\u201d answers to questions on method sound-ness and reproducibility) is the progression from the identification of contigs with mitochondrial homology to the \u201ccomplete\u201d genomes.  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for identifying this lack of methodological detail. The Methods section has been substantially expanded to explain the progression from mitochondrial-contig identification to the final selected assemblies. The revised workflow now describes organelle-specific reassembly with GetOrganelle, inspection of assembly graphs, comparison with the original SPAdes\/BLASTN reconstructions, reciprocal sequence comparisons, read-mapping validation, and circular-junction assessment. We also revised the title and adopted conservative assembly classifications: three sequences are now described as complete circular mitogenomes, whereas A. luctuosus is described as a near-complete, non-circularized mitochondrial scaffold with an incompletely recovered control region.<\/i>  How many, if any, of these contigs were complete assemblies? I would guess quite possibly none, but if they did obtain single contig mitochondria from the assembly this should be stated.&nbsp; And if multiple contigs, how many?  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for this question. The original SPAdes\/BLASTN analysis did not by itself establish complete mitochondrial genomes and was therefore retained only for assembly comparison. In the revised GetOrganelle analysis, one mitochondrial sequence was recovered per sample: three single circular assemblies (Apiomerus sp., A. ochropterus, and A. nitidicollis) and one single non-circular scaffold (A. luctuosus). This distinction is now stated explicitly in the Methods and Results.<\/i>  And what approach did the authors take to gap-filling. Ideally the location of contig breaks would be indicated on the synteny figures.  \n<b><i>Response: <\/i><\/b>\n<i>No manual gap filling or insertion of ambiguous bases was performed. Final sequences were recovered from GetOrganelle assembly paths and evaluated using the assembly graph and read support. Because the original SPAdes contigs were retained only for comparison, their breakpoints are not shown in the final synteny figures. The unresolved termini of the non-circular A. luctuosus scaffold are now indicated explicitly.<\/i>  Although synteny is well-conserved in this study, interpretation of the differences in the \n<i>Apiomerus<\/i>&nbsp; sp. accession, which one would assume are derived, would be perhaps be modulated by contig breaks in the vicinity of those differences.  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for this important observation. The original Apiomerus sp. reconstruction was indeed affected by assembly discontinuities near the region showing the apparent differences. We therefore reassembled the mitochondrial genome using GetOrganelle and validated the selected sequence through assembly-graph inspection and read remapping. The revised Apiomerus sp. mitogenome was recovered as a complete circular sequence with continuous coverage across the circular junction and the full complement of 13 protein-coding genes, 22 tRNAs, and two rRNAs. After reannotation and manual curation, the previously inferred differences were no longer supported. The four Apiomerus assemblies now show complete conservation of gene content, gene order, and transcriptional orientation, with no evidence of derived rearrangements in Apiomerus sp.<\/i>  Did the authors consider mapping the WGS data back to the assembled genomes? I ask in case there was any evidence of heteroplasmy and\/or whether this might have resolved some of the ambiguity in the Apiomerus sp. accession. It may also have revealed any need for polishing of the resulting assemblies.  \n<b><i>Response<\/i><\/b>\n<i>: We thank the reviewer for this suggestion. We mapped the original paired-end reads to both assembly versions and evaluated coverage, properly paired reads, alignment errors, and high-confidence read\u2013assembly differences. The results supported the selected GetOrganelle assemblies, resolved the previous ambiguity in Apiomerus sp., and did not indicate heteroplasmy or a need for further sequence polishing.<\/i>  Minor comments I suggest not including the \u201cHahn\u201d taxonomic in the abstract. Also, it is my understanding that \u201cbee-assassin\u201d is more commonly used than \u201cbee-killer\u201d.  \n<b>Response:<\/b> \n<i>We thank the reviewer for this suggestion. We removed the taxonomic authority \u201cHahn\u201d from the Abstract and replaced \u201cbee-killer\u201d with the more commonly used term \u201cbee-assassin.\u201d<\/i>  \u201csingle-locus markers such as cox1 and 16S rRNA\u2026\u201d.&nbsp; COI might be a more familiar way to express cox1 given its extensive use in barcoding. I see that you acknowledge naming alternatives for many of these markers later.  \n<b><i>Response:<\/i><\/b>\n<i> We thank the reviewer for the suggestion. We now introduce the marker as \u201cCOI (cox1)\u201d at first mention, while retaining cox1 in annotation-focused Methods and figures for consistency with standardized mitochondrial gene nomenclature.<\/i>  Can a key be included for the bootstrap significance symbols in Figure 1? And\/or include qualifiers for \u201chigh\u201d and \u201cmoderate\u201d in the final paragraph of the text.  \n<b><i>Response<\/i><\/b>\n<i>: We thank the reviewer for this suggestion. We added a key to Fig. 2c defining bootstrap support as high (\u226590%), moderate (70\u201389%), or low (&lt;70%). Support is indicated by color-coded node symbols rather than numerical values to maintain figure clarity.<\/i>","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-comment-16855","order":1,"name":"referee-comment-16855","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.198144.r494389, Rui Alves, University of Lleida, Lleida, 16 Jul 2026, version 1, 3 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-921\/v1#referee-response-494389","order":2,"name":"referee-response-494389","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Andr&eacute;s G&oacute;mez-Palacio<\/b>; \n<i>Posted: 05 Aug 2026<\/i>; Dr. Rui Alves  \n<i><u>We sincerely thank you for the detailed and constructive assessment of our manuscript, particularly the recommendations concerning assembly reproducibility, validation, and reporting. Each comment and concern is addressed individually in the point-by-point responses below.<\/u><\/i>  This manuscript presents the first mitochondrial genomes for four Apiomerus species and makes these data publicly available. The specimens are vouchered, the data are deposited in GenBank and the SRA, and the phylogenetic analysis broadly supports previous relationships within Harpactorinae. These are valuable contributions.  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for recognizing the value of the vouchered specimens, public data deposition, and phylogenetic contribution of this study.<\/i>  Still, my &quot;partial&quot; score has to do with the fact that the workflow from shallow whole-genome sequencing to &quot;complete mitochondrial genomes&quot; is insufficiently documented, and several standard assembly validation steps are absent. Most concerns can be addressed through clarification, but the current description does not allow the work to be fully reproduced or independently evaluated. The authors state that reads were assembled with SPAdes, mitochondrial contigs were identified by BLAST against Agriosphodrus dohrni, and &quot;used to reconstruct complete mitochondrial genomes.&quot; Nowhere is the reconstruction process actually described.  \n<b><i>Response: <\/i><\/b>\n<i>We agree that the original reconstruction workflow was insufficiently documented. The Methods now describe the complete progression from filtered reads to the selected assemblies, including GetOrganelle reassembly, assembly-graph inspection, comparison with the original SPAdes\/BLASTN reconstructions, read mapping, coverage and variant assessment, and circular-junction validation. The revised manuscript now classifies three assemblies as complete circular mitogenomes and A. luctuosus as a near-complete non-circularized scaffold. <\/i>  Also, a more complete explicit description of the results would help. Was each mitogenome recovered as a single circular contig? If not, how many mitochondrial contigs were obtained? How were contigs ordered? Were overlaps used? Were reference-guided joins employed? Was manual editing performed? Were gaps present? Were ambiguous bases introduced? One assembly is only 13.6 kb, way, shorter than the others. Comments on this? Is the control region missing?&nbsp; Were you able to circularize? You should also report on statistics for mapping reads back to the assembly, average and minimum read depth, show coverage plots, systematically identify of poorly supported regions. Also, did you polish the genome? Given that you are deviating from what are now standard practices, it would be nice to compare your assembly to one of the following: GetOrganelle, MitoZ, NOVOPlasty, or MitoFinder!  \n<b><i>Response: <\/i><\/b>\n<i>We thank the reviewer for these detailed suggestions. We reassembled all samples with GetOrganelle and expanded the Methods and Results accordingly. A. ochropterus, A. nitidicollis, and Apiomerus sp. were recovered as single circular assemblies, whereas A. luctuosus remained a single gap-free, non-circularized scaffold with an incompletely recovered control region. No reference-guided joins, manual gap filling, gaps, or ambiguous bases were introduced. The final assemblies were validated by read remapping, coverage and variant analyses, and circular-junction support; these results and coverage summaries are now presented in Fig. 1. The read evidence did not indicate a need for additional polishing.<\/i>  Coverage estimates are also unclear and hard to interpret and compare between nuclear and mitogenomes. Please also provide, N50, longest contig, mitochondrial contig length, etc. What was the final partitioning scheme and substitution models in IQ Tree? Figure 1 displays bootstrap values. Were SH-aLRT values omitted intentionally?  \n<b><i>Response:&nbsp;<\/i><\/b>\n<i>We thank the reviewer. Coverage terminology and assembly statistics were clarified in Tables 1 and 2. The Methods now specify the 13 initial PCG partitions, partitioned model selection under MFP+MERGE, 1,000 ultrafast bootstrap replicates, and 1,000 SH-aLRT replicates. SH-aLRT values were calculated but intentionally omitted from Fig. 2c; the main figure displays only ultrafast-bootstrap support categories for clarity.<\/i>","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-comment-16856","order":3,"name":"referee-comment-16856","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.208114.r514759, Carlos Eduardo Almeida, Universidade Federal de S\u00e3o Jo\u00e3o del Rei, Campus Centro-Oeste \u201cDona Lindu\u201d, Divin\u00f3polis, 21 Sep 2026, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-response-514759","order":4,"name":"referee-response-514759","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.208114.r522072, Feiyun Tu, Hainan Normal University, Haikou, Hainan, 22 Sep 2026, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-response-522072","order":5,"name":"referee-response-522072","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.208114.r518524, Kanishka Senevirathna, University of Alberta, Edmonton, 28 Sep 2026, version 2, indexed","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-response-518524","order":6,"name":"referee-response-518524","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Andr&eacute;s G&oacute;mez-Palacio<\/b>; \n<i>Posted: 28 Sep 2026<\/i>; We thank the reviewer for the additional comments and for their consideration of our Genome Note. We have carefully evaluated each point. As detailed below, several suggestions concern presentation preferences or additional information beyond the intended scope of the Genome Note rather than issues affecting the validity or reproducibility of the mitochondrial genome resources reported in Version 2. The article has now formally passed peer review, and we therefore do not consider that these points warrant preparation of an additional version at this stage.  \n<b>Comment 1.<\/b> \n<i>The specimen collection details [...] are currently presented as a single continuous paragraph [...] I suggest presenting these data as a table.<\/i>  \n<b>Response:<\/b> We thank the reviewer for this suggestion. The collection information is already provided in the \n<i>Sampling and biological material<\/i> section, including the relevant specimen, voucher, collection, preservation, locality, and repository information. Presenting these data in a table would constitute an alternative formatting choice rather than provide additional information or affect the reproducibility of the work. We therefore prefer to retain the current concise presentation, which is consistent with the Genome Note format.  \n<b>Comment 2.<\/b> \n<i>Could the authors briefly explain why A. ochropterus needed a longer digestion and two elutions? [...] it would be helpful to report the actual DNA concentrations and purity ratios (260\/280 and 260\/230) for each sample in Table 1.<\/i>  \n<b>Response:<\/b> We appreciate this observation. The extraction modifications applied to \n<i>A. ochropterus<\/i> are already reported to ensure methodological transparency and reflect the sample-specific optimization performed during DNA extraction. We do not consider it appropriate to infer retrospectively that these modifications resulted specifically from low DNA yield or specimen condition unless this was experimentally established. Likewise, the manuscript reports the quality criteria and sequencing\/assembly information relevant to the generation and assessment of the mitochondrial assemblies. Additional spectrophotometric measurements are not required to establish the validity of the reported assemblies, and their absence cannot by itself be used to infer the cause of the incomplete \n<i>A. luctuosus<\/i> assembly. We therefore do not consider further modification necessary.  \n<b>Comment 3.<\/b> \n<i>Every conclusion [...] rests on a single specimen per species [...] the manuscript should explicitly acknowledge this as a limitation.<\/i>  \n<b>Response:<\/b> We agree that each mitochondrial assembly was generated from a single voucher specimen. However, this is explicit from the sampling design and is consistent with the purpose of this Genome Note, which reports mitochondrial genomic resources from individually identified and vouchered specimens rather than assessing intraspecific mitochondrial variation. The phylogenetic analysis was performed to evaluate the placement of the newly generated mitochondrial sequences relative to available Reduviidae mitogenomes, not to characterize within-species diversity or population-level variation. Accordingly, the phylogenetic placement reported for each sequence pertains to the analyzed voucher and is not intended to represent the full mitochondrial diversity of the corresponding species. We therefore do not consider the single-voucher design to constitute an unreported limitation requiring an additional revision.  \n<b>Comment 4.<\/b> \n<i>The authors have taken some steps to validate the mitogenome assemblies, but it would be helpful to explain how they ruled out NUMTs [...] especially important for A. luctuosus.<\/i>  \n<b>Response:<\/b> We thank the reviewer for raising this point. The study does not claim that NUMTs were categorically \u201cruled out.\u201d Rather, mitochondrial sequence identity was supported through the assembly and validation procedures described in the Methods, including organelle-targeted assembly, sequence similarity assessment, mitochondrial gene annotation and coding integrity, and comparative evaluation of mitochondrial genome organization. The inability to circularize the \n<i>A. luctuosus<\/i> assembly was therefore conservatively reported rather than interpreted as evidence for a complete mitochondrial genome. We consider that the manuscript already appropriately distinguishes the evidence supported by the sequence data from conclusions that cannot be established from these data alone.  \n<b>Comment 5.<\/b> \n<i>The manuscript would benefit from a short Discussion section [...] compare genome sizes and AT content [...] discuss the phylogenetic results [...] suggest future work.<\/i>  \n<b>Response:<\/b> We respectfully disagree that a conventional Discussion section is required for this article. The manuscript was submitted specifically as a \n<b>Genome Note<\/b>, whose purpose is the concise reporting and characterization of genomic resources rather than a conventional research article providing an extended comparative Discussion. The requested comparisons, broader biological interpretation, and proposed future research would substantially extend the intended scope of this article type. We have therefore retained the focused Genome Note structure.  \n<b>Comment 6.<\/b> \n<i>Table 1 caption says \u201cRead-processing and SPAdes-based whole-genome assembly statistics\u201d [...] clarify the caption wording so it doesn't imply whole-nuclear-genome assembly stats are reported.<\/i>  \n<b>Response:<\/b> We appreciate this wording observation. In context, the term refers to the initial assembly step described in the Methods and does not indicate that Table 1 reports a characterization of the nuclear genome. The subsequent mitochondrial sequence identification and organelle-specific assembly workflow are explicitly described in the manuscript. We agree that alternative wording could further distinguish these stages; however, this terminological point does not affect the reported data or their interpretation, and we do not consider it sufficient to warrant an additional article version after completion of peer review.","URL":"https:\/\/f1000research.com\/articles\/15-921\/v2#referee-comment-17264","order":7,"name":"referee-comment-17264","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The author(s) declared that no grants were involved in supporting this work","order":8,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}