{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:11:54Z","timestamp":1772169114996,"version":"3.50.1"},"reference-count":38,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["220540"],"award-info":[{"award-number":["220540"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218328"],"award-info":[{"award-number":["218328"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    We present a genome assembly from an individual male\n                    <ns3:italic>Xyphosia miliaria<\/ns3:italic>\n                    (tephritid fruit fly; Arthropoda; Insecta; Diptera; Tephritidae). The assembly contains two haplotypes with total lengths of 806.98 megabases and 799.90 megabases. Most of haplotype 1 (97.34%) is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. Most of haplotype 2 (83.09%) is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.41 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain\u202fand\u202fIreland.\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.25047.1","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:40:19Z","timestamp":1761061219000},"page":"585","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["The genome sequence of a tephritid fruit fly, Xyphosia miliaria (Schrank, 1781) (Diptera: Tephritidae)"],"prefix":"10.12688","volume":"10","author":[{"given":"Ryan","family":"Mitchell","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6380-0329","authenticated-orcid":false,"given":"Liam M.","family":"Crowley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"McCulloch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1255-0045","authenticated-orcid":false,"given":"Olga","family":"Sivell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Natural History Museum Genome Acquisition Lab","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"University of Oxford and Wytham Woods Genome Acquisition Lab","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Wellcome Sanger Institute Scientific Operations: Sequencing Operations","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Wellcome Sanger Institute Tree of Life Core Informatics team","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Tree of Life Core Informatics collective","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"Darwin Tree of Life Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"892-905","DOI":"10.1111\/1755-0998.13160","article-title":"MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.","volume":"20","author":"R Allio","year":"2020","journal-title":"Mol Ecol 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Li","year":"2018","journal-title":"Bioinformatics."},{"key":"ref-24","doi-asserted-by":"publisher","first-page":"4647-4654","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.","volume":"38","author":"M Manni","year":"2021","journal-title":"Mol Biol Evol."},{"key":"ref-25","article-title":"Docker: lightweight Linux containers for consistent development and deployment.","volume":"2014","author":"D Merkel","year":"2014","journal-title":"Linux J."},{"key":"ref-26","article-title":"Xyphosia miliaria (Schrank, 1781)","year":"2025"},{"key":"ref-27","first-page":"33-69","article-title":"Studies on the biology and larval morphology of some Trypetidae (Dipt.).","volume":"28","author":"P Persson","year":"1963","journal-title":"Opuscula Entomol."},{"key":"ref-28","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.","volume":"11","author":"T Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"1665-1680","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.","volume":"159","author":"S Rao","year":"2014","journal-title":"Cell."},{"key":"ref-30","doi-asserted-by":"publisher","first-page":"737-746","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species.","volume":"592","author":"A Rhie","year":"2021","journal-title":"Nature."},{"key":"ref-31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.","volume":"21","author":"A Rhie","year":"2020","journal-title":"Genome Biol."},{"key":"ref-32","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baaa062","article-title":"NCBI Taxonomy: a comprehensive update on curation, resources and tools.","volume":"2020","author":"C Schoch","year":"2020","journal-title":"Database (Oxford)."},{"key":"ref-33","doi-asserted-by":"publisher","first-page":"339","DOI":"10.12688\/wellcomeopenres.21143.1","article-title":"A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life project [version 1; peer review: 2 approved].","volume":"9","author":"A Twyford","year":"2024","journal-title":"Wellcome Open Res."},{"key":"ref-34","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-023-05385-y","article-title":"MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.","volume":"24","author":"M Uliano-Silva","year":"2023","journal-title":"BMC Bioinformatics."},{"key":"ref-35","doi-asserted-by":"publisher","first-page":"314-324","DOI":"10.1109\/IPDPS.2019.00041","article-title":"Efficient architecture-aware acceleration of BWA-MEM for multicore systems.","author":"M Vasimuddin","year":"2019"},{"key":"ref-36","doi-asserted-by":"publisher","first-page":"1063-71","DOI":"10.1111\/j.1365-2656.2008.01406.x","article-title":"The relative importance of resources and natural enemies in determining herbivore abundance: thistles, tephritids and parasitoids.","volume":"77","author":"M Walker","year":"2008","journal-title":"J Anim Ecol."},{"key":"ref-37","article-title":"Tephritid flies.","volume":"10","author":"I White","year":"1988"},{"key":"ref-38","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: Yet another Hi-C Scaffolding tool.","volume":"39","author":"C Zhou","year":"2023","journal-title":"Bioinformatics."}],"container-title":["Wellcome Open 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.27613.r140480, Daubian Santos, Universidade Federal do ABC, Santo Andr\u00e9, State of S\u00e3o Paulo, 25 Nov 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-585\/v1#referee-response-140480","order":0,"name":"referee-response-140480","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.27613.r140485, Matsapume Detcharoen, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand, Hat Yai, 29 Dec 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-585\/v1#referee-response-140485","order":1,"name":"referee-response-140485","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (220540) and the Darwin Tree of Life Discretionary Award [218328, &#60;a href=https:\/\/doi.org\/10.35802\/218328&#62;https:\/\/doi.org\/10.35802\/218328 &#60;\/a&#62;]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"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"}]}}