{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T15:00:11Z","timestamp":1790262011162,"version":"4.1.0"},"reference-count":87,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,16]],"date-time":"2024-11-16T00:00:00Z","timestamp":1731715200000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMTs) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false-positive detection of NUMTs is common when handling repeat-rich sequences, while fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10\u00d7 linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n = 5,310), indicating the gene-containing regions were well assembled. We used 3 complementary methods (NUMTFinder, dinumt, and PALMER) to study the NUMT landscape of the cane toad genome. All 3 methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.<\/jats:p>","DOI":"10.1093\/gbe\/evae246","type":"journal-article","created":{"date-parts":[[2024,11,15]],"date-time":"2024-11-15T07:23:45Z","timestamp":1731655425000},"source":"Crossref","is-referenced-by-count":2,"title":["Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9041-8964","authenticated-orcid":false,"given":"Kelton","family":"Cheung","sequence":"first","affiliation":[{"name":"Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales , Sydney ,","place":["Australia"]},{"name":"Evolution & Ecology Research Centre, School of Biotechnology & Biomolecular Sciences, University of New South Wales , Sydney ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3279-7005","authenticated-orcid":false,"given":"Lee Ann","family":"Rollins","sequence":"additional","affiliation":[{"name":"Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales , Sydney ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4045-4571","authenticated-orcid":false,"given":"Jillian M","family":"Hammond","sequence":"additional","affiliation":[{"name":"Genomics and Inherited Disease Program, Garvan Institute of Medical Research , Sydney, New South Wales ,","place":["Australia"]},{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute , Darlinghurst, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0410-4849","authenticated-orcid":false,"given":"Kirston","family":"Barton","sequence":"additional","affiliation":[{"name":"Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research , Sydney, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6192-6937","authenticated-orcid":false,"given":"James M","family":"Ferguson","sequence":"additional","affiliation":[{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute , Darlinghurst, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4830-4009","authenticated-orcid":false,"given":"Harrison J F","family":"Eyck","sequence":"additional","affiliation":[{"name":"National Collections and Marine Infrastructure , CSIRO, Canberra, Australian Capital Territory ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7529-5657","authenticated-orcid":false,"given":"Richard","family":"Shine","sequence":"additional","affiliation":[{"name":"School of Natural Sciences, Macquarie University , Sydney, New South Wales ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3645-5539","authenticated-orcid":false,"given":"Richard J","family":"Edwards","sequence":"additional","affiliation":[{"name":"Evolution & Ecology Research Centre, School of Biotechnology & Biomolecular Sciences, University of New South Wales , Sydney ,","place":["Australia"]},{"name":"Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia , Western Australia ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,11,16]]},"reference":[{"issue":"7366","key":"2024112923161799500_evae246-B1","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nature10390","article-title":"The genome of the green anole lizard and a comparative analysis with birds and mammals","volume":"477","author":"Alfoldi","year":"2011","journal-title":"Nature"},{"issue":"3","key":"2024112923161799500_evae246-B2","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1007\/BF00325949","article-title":"Specific nuclear DNA amounts in toads of the genus Bufo","volume":"29","author":"Bachmann","year":"1970","journal-title":"Chromosoma"},{"issue":"1","key":"2024112923161799500_evae246-B3","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1146\/annurev.ecolsys.36.091704.175513","article-title":"The population biology of mitochondrial DNA and its phylogenetic implications. 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