{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T12:05:25Z","timestamp":1753877125853,"version":"3.41.2"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T00:00:00Z","timestamp":1738195200000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Mitochondrial genomes are a rich source of data for various downstream analyses such as population genetics, phylogeny, and systematics. Today it is possible to assemble rapidly large numbers of mitogenomes, mainly employing next-generation sequencing and third-generation sequencing. However, verification of the correctness of the generated sequences is often lacking, especially for noncoding, length-variable parts. Here we have assembled the mitochondrial genome (mitogenome) from four specimens of Agabus bipustulatus (L.) using long-read nanopore sequence data. The use of the latest nanopore chemistry (V14) combined with a comprehensive error correction workflow enabled the generation of mitogenomes with high accuracy and reproducibility, as tested on four samples. The resulting mitogenome is 17,876\u00a0bp long, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Differences in the control region length between samples were minimal. The arrangement of protein-coding genes, transfer RNAs, and ribosomal RNAs is similar to that of the ancestral insect mitogenome. Finally, we used the assembled, well-supported mitogenomes in the phylogenetic analysis of a part of the Dytiscidae related to the studied species and confronted the results with previous hypotheses. Conflicting estimates of their phylogeny suggest that considerably more robust data are required for a plausible sketch of their evolutionary history. Our research has confirmed that readily available third-generation sequencing technologies, such as Oxford Nanopore Technologies, combined with long-read sequencing, offer a highly efficient, reliable, and cost-effective approach to generate complete mitogenomes and potentially other longer regions of the genome. The use of reliable data will ultimately contribute to a deeper understanding and improved conservation strategies for diving beetles and other organisms.<\/jats:p>","DOI":"10.1093\/jisesa\/ieaf009","type":"journal-article","created":{"date-parts":[[2025,1,30]],"date-time":"2025-01-30T06:58:33Z","timestamp":1738220313000},"source":"Crossref","is-referenced-by-count":0,"title":["Multi-sample long-read nanopore sequencing of <i>Agabus bipustulatus<\/i> (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1020-7331","authenticated-orcid":false,"given":"Olena","family":"Bielikova","sequence":"first","affiliation":[{"name":"Laboratory of molecular genetic research,\u00a0Institute of Fisheries of the National Academy of Agrarian Sciences of Ukraine , Kyiv ,","place":["Ukraine"]},{"name":"ZooLab, Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences , Bratislava ,","place":["Slovakia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ondrej","family":"Vargov\u010d\u00edk","sequence":"additional","affiliation":[{"name":"ZooLab, Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences , Bratislava ,","place":["Slovakia"]},{"name":"Department of Ecology, Faculty of Natural Sciences, Comenius University , Bratislava ,","place":["Slovakia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0506-6212","authenticated-orcid":false,"given":"Zuzana","family":"\u010ciamporov\u00e1-Za\u0165ovi\u010dov\u00e1","sequence":"additional","affiliation":[{"name":"ZooLab, Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences , Bratislava ,","place":["Slovakia"]},{"name":"Department of Ecology, Faculty of Natural Sciences, Comenius University , Bratislava ,","place":["Slovakia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6269-3592","authenticated-orcid":false,"given":"Fedor","family":"\u010ciampor","sequence":"additional","affiliation":[{"name":"ZooLab, Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences , Bratislava ,","place":["Slovakia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,1,30]]},"reference":[{"key":"2025013006581619700_CIT0001","doi-asserted-by":"publisher","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"Afgan","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025013006581619700_CIT0002","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.ympev.2016.09.024","article-title":"Accurate annotation of protein-coding genes in mitochondrial genomes","volume":"106","author":"Al Arab","year":"2017","journal-title":"Mol. 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