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Whilst species of\n                    <jats:italic>Ascaris<\/jats:italic>\n                    are morphologically indistinguishable, analysis of mitochondrial loci has revealed three clades (A, B, C) broadly associated with host species and geographic distribution. The diversity within these lineages may expand with the addition of further genomic data. Here, we present a bioinformatic framework for\n                    <jats:italic>de novo<\/jats:italic>\n                    assembly of complete mitochondrial genomes (mitogenomes) from low-coverage whole-genome data through host-read depletion or mtDNA read enrichment, followed by mtDNA-specific assembly. Our approach yielded 149 high-quality\n                    <jats:italic>Ascaris<\/jats:italic>\n                    mitogenome assemblies, enabling the study of population-level diversity, including the identification of a novel clade (Clade D, designated here) associated with human samples from Ethiopia. Our analysis further revealed Clade C to comprise of pig-derived samples from Europe based on characterisation of worms isolated in Germany. The methods described here provide a scalable framework for mitogenome reconstruction with insights into roundworm population-genomic and phylogenetic studies.\n                  <\/jats:p>","DOI":"10.1038\/s41598-026-65562-w","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T09:18:11Z","timestamp":1789118291000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Scalable assembly of Ascaris mitogenomes from whole-genome data reveals a novel clade"],"prefix":"10.1038","volume":"16","author":[{"given":"Lauren","family":"Woolfe","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kezia","family":"Kozel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Poom","family":"Adisakwattana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allen Jethro","family":"Alonte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kennesa Klariz","family":"Llanes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Juh\u00e1sz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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