{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T13:33:29Z","timestamp":1793021609608,"version":"4.5.0"},"reference-count":47,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":5,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32325010"],"award-info":[{"award-number":["32325010"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Nuclear mitochondrial DNA segments (NUMTs) are genomic DNA fragments that originate from historical insertions of mitochondrial DNA sequences into the nuclear genome. During mitochondrial genome (mtgenome) assembly from short\u2010read genome sequencing data, NUMT fragments may be misidentified and incorporated into mtgenome assemblies, leading to NUMT contamination. Although some assembly programs include steps to filter NUMTs, these approaches are not always effective. Here, we present MitoNumt, a multifunctional workflow. Using this pipeline, we recovered mtgenomes, complete NUMT (coexistence with the mtgenomes), and incomplete NUMT fragments from PacBio HiFi long\u2010read sequencing data for five species of the genus\n                    <jats:italic>Panthera<\/jats:italic>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Puma concolor<\/jats:italic>\n                    <\/jats:styled-content>\n                    . We then used these sequences to check mtgenomes available in the NCBI database. NUMT contamination was detected in mtgenomes from all\n                    <jats:italic>Panthera<\/jats:italic>\n                    species examined, with 23 contaminated mtgenomes identified and contamination lengths ranging from 3 to 416\u2009bp. In addition, phylogenetic trees reconstructed from NUMT fragments of at least 5000\u2009bp consistently recovered a topology congruent with the currently accepted\n                    <jats:italic>Panthera<\/jats:italic>\n                    phylogeny. Overall, this workflow enables the identification of HiFi\u2010supported mtgenomes and complete NUMTs, and the detection of NUMT contamination in assembled mtgenomes, thereby improving the reliability of mtgenome\u2010based evolutionary and genetic studies.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70211","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:48:43Z","timestamp":1791355723000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>MitoNumt<\/scp>\n                    : A Workflow for Recovering Mitochondrial Genomes From Long\u2010Read Data and Detecting\n                    <scp>NUMT<\/scp>\n                    Contamination in Mitochondrial Genome Assemblies"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4474-9596","authenticated-orcid":false,"given":"Ruidong","family":"Cao","sequence":"first","affiliation":[{"name":"State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences  Beijing China"},{"name":"University of Chinese Academy of Sciences  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Xin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences  Beijing China"},{"name":"University of Chinese Academy of Sciences  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yubo","family":"Hao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences  Beijing China"},{"name":"University of Chinese Academy of Sciences  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3409-3164","authenticated-orcid":false,"given":"Yibo","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences  Beijing China"},{"name":"University of Chinese Academy of Sciences  Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,6]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010017\u20101927\u2010y"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365\u2010294X.2003.02063.x"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0169\u20105347(01)02151\u20106"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mito.2010.10.004"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.3109\/19401736.2014.926483"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/inc3.70032Digital"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mito.2020.09.001"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1038"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw955"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evac059"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msag049"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt371"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000834"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aax5751"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2005.08.023"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae263"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186668.114"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2025.116110"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evaf174"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.1006\/geno.1996.0188"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz173"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/0169\u20105347(94)90057\u20104"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm248"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00239\u2010005\u20100259\u20100"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msh110"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syaf021"},{"key":"e_1_2_11_31_1","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.191"},{"key":"e_1_2_11_32_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0803076105"},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esad082"},{"key":"e_1_2_11_34_1","doi-asserted-by":"publisher","DOI":"10.1155\/2024\/2174469"},{"key":"e_1_2_11_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbs017"},{"key":"e_1_2_11_36_1","doi-asserted-by":"publisher","DOI":"10.1080\/10635150701311362"},{"key":"e_1_2_11_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks424"},{"key":"e_1_2_11_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msad278"},{"key":"e_1_2_11_39_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592\u2010024\u201001658\u2010y"},{"key":"e_1_2_11_40_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592\u2010024\u201001658\u2010y"},{"key":"e_1_2_11_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010022\u201005288\u20107"},{"key":"e_1_2_11_42_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4997"},{"key":"e_1_2_11_43_1","doi-asserted-by":"publisher","DOI":"10.3390\/biom13050753"},{"key":"e_1_2_11_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac111"},{"key":"e_1_2_11_45_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syag012"},{"key":"e_1_2_11_46_1","doi-asserted-by":"publisher","DOI":"10.3390\/d17090634"},{"key":"e_1_2_11_47_1","doi-asserted-by":"publisher","DOI":"10.1111\/1755\u20100998.13669Digital"},{"key":"e_1_2_11_48_1","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.70095"}],"container-title":["Molecular 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