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We analyzed 40 species representing the major extant lineages of Elatostemateae using complete plastomes and nuclear ribosomal DNA (nrDNA);\n                    <jats:italic>Metapilea<\/jats:italic>\n                    was excluded because suitable DNA material was unavailable. Plastomes retained the typical angiosperm quadripartite structure and ranged from 143,738 to 163,969\u2009bp. Comparative analyses revealed large inversions in the large single\u2010copy (LSC) region, pronounced inverted\u2010repeat (IR) boundary shifts, and a rare plastid mitochondrial DNA\u2010derived sequence (PTMT) insertion. Seven highly variable regions were identified as candidate markers for DNA barcoding. Plastome, protein\u2010coding sequence (CDS), nrDNA, and combined analyses recovered the same three major Elatostemateae clades, although several internal nrDNA nodes had lower support. Plastid and nrDNA data placed\n                    <jats:italic>Gyrotaenia<\/jats:italic>\n                    as sister to\n                    <jats:italic>Pilea s.l<\/jats:italic>\n                    . within Elatostemateae, whereas recent low\u2010copy nuclear evidence places\n                    <jats:italic>Gyrotaenia<\/jats:italic>\n                    \u2009+\u2009\n                    <jats:italic>Myriocarpa<\/jats:italic>\n                    sister to core Elatostemateae, revealing cytonuclear discordance. These results provide a framework for Elatostemateae systematics and document substantial plastome structural variation; denser low\u2010copy nuclear or whole\u2010genome sampling will be needed to distinguish incomplete lineage sorting from historical introgression.\n                  <\/jats:p>","DOI":"10.1002\/ece3.74416","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T01:03:01Z","timestamp":1791334981000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plastid Phylogenomics of Elatostemateae (Urticaceae): Insights Into Structural Variation and Phylogenetic Relationships"],"prefix":"10.1002","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8708-4718","authenticated-orcid":false,"given":"Long\u2010Fei","family":"Fu","sequence":"first","affiliation":[{"name":"Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany  Guilin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi\u2010Bing","family":"Xin","sequence":"additional","affiliation":[{"name":"Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany  Guilin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Xiong","sequence":"additional","affiliation":[{"name":"Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany  Guilin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Wen","sequence":"additional","affiliation":[{"name":"Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany  Guilin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi\u2010Gang","family":"Wei","sequence":"additional","affiliation":[{"name":"Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany  Guilin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre K.","family":"Monro","sequence":"additional","affiliation":[{"name":"Identification &amp; Naming Department The Royal Botanic Gardens, Kew  Richmond UK"}],"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":"crossref","first-page":"562","DOI":"10.1007\/s00239-020-09958-w","article-title":"Complete Chloroplast Genomes of Anthurium Huixtlense and Pothos Scandens (Pothoideae, Araceae): Unique Inverted Repeat Expansion and Contraction Affect Rate of Evolution","volume":"88","author":"Abdullah","year":"2020","journal-title":"Journal of Molecular Evolution"},{"key":"e_1_2_11_3_1","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1890\/13-1452.1","article-title":"Model Selection for Ecologists: The Worldviews of AIC and BIC","volume":"95","author":"Aho K.","year":"2014","journal-title":"Ecology"},{"key":"e_1_2_11_4_1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem Repeats Finder: A Program to Analyze DNA Sequences","volume":"27","author":"Benson G.","year":"1999","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A Tool for Automated Alignment Trimming in Large\u2010Scale Phylogenetic Analyses","volume":"25","author":"Capella\u2010Guti\u00e9rrez S.","year":"2009","journal-title":"Bioinformatics"},{"key":"e_1_2_11_6_1","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evab215","article-title":"Plastome Structural Evolution and Homoplastic Inversions in Neo\u2010Astragalus (Fabaceae)","volume":"13","author":"Charboneau J. 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