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Despite advances in phylogenomics, resources available for reconstructing regional phylogenies are still largely incomplete and poorly resolved at the species level. We developed a workflow to assemble a phylogenetic dataset for a regional flora using Angiosperms353 target\u2010enrichment and high\u2010throughput genome sequencing. We sampled tissues from freshly collected plants and herbarium specimens representing the angiosperm diversity of the Geneva canton in Switzerland (1098 species). We used ORTHOSKIM to recover targeted nuclear genes and plastid loci from off\u2010target reads, estimated relationships and time divergence using IQTREE, weighted\u2010ASTRAL and treePL, and compared the results obtained from nuclear and plastid genes. We recovered a mean of 289 nuclear and 54 plastid genes for 1316 taxa, representing 92% of the species native to the Geneva canton. We demonstrate that nuclear genes provide increased resolution and phylogenetic support, but similar divergence time estimates compared to plastomes. Our workflow based on Angiosperms353 data provides a phylogenetic framework for an entire regional flora that is consistent with current systematic knowledge and more resolved and complete at the infrageneric level than trees obtained from phylogenetic resources available for angiosperms. This type of genomic data opens perspectives for fine\u2010scale biodiversity and conservation research that integrates evolutionary history.<\/jats:p>","DOI":"10.1111\/1755-0998.70202","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T17:31:12Z","timestamp":1790616672000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Simultaneous Inference of Flora\u2010Wide Nuclear and Plastid Phylogenies Using Angiosperms353 Sequence Capture Data"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9285-2505","authenticated-orcid":false,"given":"S\u00e9bastien","family":"Miche","sequence":"first","affiliation":[{"name":"Department of Plant Sciences University of Geneva  Geneva Switzerland"},{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7766-3732","authenticated-orcid":false,"given":"Charles","family":"Pouchon","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Geneva  Geneva Switzerland"},{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0517-4731","authenticated-orcid":false,"given":"Camille","family":"Christe","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Geneva  Geneva Switzerland"},{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2450-2879","authenticated-orcid":false,"given":"Anna","family":"Marcionetti","sequence":"additional","affiliation":[{"name":"Department of Computational Biology University of Lausanne  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7144-5134","authenticated-orcid":false,"given":"Maya","family":"Wells","sequence":"additional","affiliation":[{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6784-8565","authenticated-orcid":false,"given":"Yamama","family":"Naciri","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Geneva  Geneva Switzerland"},{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7269-4281","authenticated-orcid":false,"given":"Nicolas","family":"Wyler","sequence":"additional","affiliation":[{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2021-114X","authenticated-orcid":false,"given":"Mathieu","family":"Perret","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Geneva  Geneva Switzerland"},{"name":"Jardin Botanique de Gen\u00e8ve  Chamb\u00e9sy Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2018.12.002"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2023.0017"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/plants9040432"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.01407"},{"key":"e_1_2_12_6_1","unstructured":"Andrews S.2010.\u201cFastQC: A Quality Control Analysis Tool for High Throughput Sequencing Data.\u201dhttps:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajb2.1697"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1713819115"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syab035"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajb2.1703"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1095-8339.2003.00157.x"},{"key":"e_1_2_12_12_1","unstructured":"BDM Coordination Office.2014.\u201cSwiss Biodiversity Monitoring BDM. 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