{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T03:12:17Z","timestamp":1777950737632,"version":"3.51.4"},"reference-count":57,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:00:00Z","timestamp":1773964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:00:00Z","timestamp":1773964800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["11Q4724N"],"award-info":[{"award-number":["11Q4724N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000155","name":"Division of Environmental Biology","doi-asserted-by":"publisher","award":["DEB\u20102331644"],"award-info":[{"award-number":["DEB\u20102331644"]}],"id":[{"id":"10.13039\/100000155","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":[[2026,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information\u2010rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed\u2010species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high\u2010abundance bloom samples, we recovered complete plastomes of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Stephanodiscus hantzschii<\/jats:italic>\n                    <\/jats:styled-content>\n                    with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non\u2010bloom sample, we reconstructed a potentially novel\n                    <jats:italic>Cyclotella<\/jats:italic>\n                    plastome with only 94.0% identity to its closest available reference,\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Cyclotella atomus<\/jats:italic>\n                    <\/jats:styled-content>\n                    . Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species\u2010level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70128","type":"journal-article","created":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T08:07:11Z","timestamp":1773994031000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in\n                    <scp>eDNA<\/scp>\n                    Metagenomic Data"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5709-3004","authenticated-orcid":false,"given":"Manon Mireille","family":"Geerts","sequence":"first","affiliation":[{"name":"Eco\u2010Evo\u2010Devo and Conservation of Fishes, Department of Biology KU Leuven  Leuven Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1630-4653","authenticated-orcid":false,"given":"Manuel","family":"Curto","sequence":"additional","affiliation":[{"name":"CIBIO\u2013Research Center in Biodiversity and Genetic Resources University of Porto  Vair\u00e3o Portugal"},{"name":"Department of Ecosystem Management, Climate and Biodiversity, Institute of Integrative Nature Conservation Research BOKU University  Vienna Austria"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning CIBIO, Campus de Vair\u00e3o  Vair\u00e3o Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1241-2654","authenticated-orcid":false,"given":"Andrew J.","family":"Alverson","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences University of Arkansas  Fayetteville Arkansas USA"}]},{"given":"Jeffery","family":"Stone","sequence":"additional","affiliation":[{"name":"Department of Earth and Environmental Systems Indiana State University  Terre Haute Indiana USA"}]},{"given":"Hugo F.","family":"Gante","sequence":"additional","affiliation":[{"name":"Eco\u2010Evo\u2010Devo and Conservation of Fishes, Department of Biology KU Leuven  Leuven Belgium"},{"name":"Department of Biology Royal Museum for Central Africa, Section Vertebrates  Tervuren Belgium"},{"name":"CE3C\u2014Centre for Ecology, Evolution and Environmental Change, Faculty of Science University of Lisbon  Lisbon 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