{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T05:14:31Z","timestamp":1790399671561,"version":"4.1.0"},"reference-count":62,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100013064","name":"Key Research and Development Program of Jiangxi Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013064","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences (\n                    <jats:italic>accD, ycf1, clpP, ndhF<\/jats:italic>\n                    , and\n                    <jats:italic>rpl22<\/jats:italic>\n                    ) and intergenic spacers (\n                    <jats:italic>rpl33-rps18<\/jats:italic>\n                    , the\n                    <jats:italic>trnG-UCC<\/jats:italic>\n                    intron,\n                    <jats:italic>trnH-GUG-psbA, accD-psaI<\/jats:italic>\n                    , and\n                    <jats:italic>petA-psbJ<\/jats:italic>\n                    ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1926463","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T06:02:50Z","timestamp":1787724170000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae"],"prefix":"10.3389","volume":"17","author":[{"given":"Sadaf","family":"Habib","sequence":"first","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences","place":["Jiujiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Shi","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences","place":["Jiujiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences","place":["Jiujiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wyckliffe Omondi","family":"Omollo","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Stevenson","sequence":"additional","affiliation":[{"name":"New York Botanical Garden","place":["Bronx, NY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinlong","family":"Li","sequence":"additional","affiliation":[{"name":"Shanxi Agricultural University","place":["Taiyuan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangjun","family":"Lai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences","place":["Beijing, China"]},{"name":"China National Botanical Garden","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Feng","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences","place":["Jiujiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1186\/s12906-018-2114-z","article-title":"Phytochemical investigation and antimicrobial appraisal of Parrotiopsis jacquemontiana (Decne) Rehder","volume":"18","author":"Ali","year":"2018","journal-title":"BMC Complement. 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