{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:59:59Z","timestamp":1790189999904,"version":"4.1.0"},"reference-count":97,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T00:00:00Z","timestamp":1777420800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"the Yunnan Province Science and Technology Talent and Platform Program-Yunnan Province Zhang Qixiang Expert Workstation","award":["202405AF140078"],"award-info":[{"award-number":["202405AF140078"]}]},{"name":"Key R&D Program of Shandong Province","award":["2025LZGC031"],"award-info":[{"award-number":["2025LZGC031"]}]},{"name":"the National Key Research and Development Project of China","award":["2023YFD1200105"],"award-info":[{"award-number":["2023YFD1200105"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Structural variations that generate novel alleles are fundamental drivers of phenotypic diversity. In crape myrtle (Lagerstroemia indica), an important summer-flowering woody species, the purple leaf trait is prized for its visual appeal and stress resistance, representing a key breeding objective. Although anthocyanin accumulation underlies purple leaf formation, its key genetic locus has remained unclear. Here, we constructed five segregated populations of crape myrtle and confirmed that the purple leaf trait is a single-gene dominant trait. Combining bulked segregant analysis with metabolomics and RNA-seq led to the identification of LiBBX16, a B-box zinc-finger transcription factor. This gene has two alleles in purple-leafed (LiBBX16p and LiBBX16a) and green-leafed (LiBBX16g and LiBBX16a) plants. LiBBX16p contains a unique 32-bp deletion causing a frameshift, premature termination, and nucleo-cytoplasmic localization. An InDel marker derived from this deletion effectively distinguished purple-leafed from green-leafed plants and identified that all plants homozygous for LiBBX16p are seedling lethal. Heterologous expression of LiBBX16p in Arabidopsis resulted in purple leaves and stems, with anthocyanin content ~9.5-fold higher than in controls. Conversely, silencing LiBBX16 in purple-leafed L. indica reduced anthocyanin content, turning leaves green. We further found that the 32-bp deletion enhances LiBBX16\u2019s activation of anthocyanin synthesis-related genes, particularly LiF3GT and LiMYB75. Mechanistically, unlike LiBBX16g, which directly binds DNA, LiBBX16p likely acts as a coactivator recruited via protein\u2013protein interactions. Overall, our results identified a neomorphic LiBBX16 allele that coregulates anthocyanin accumulation and seedling development, providing valuable insights into purple leaf formation and a target gene for molecular breeding.<\/jats:p>","DOI":"10.1093\/hr\/uhag179","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T11:52:15Z","timestamp":1777377135000},"source":"Crossref","is-referenced-by-count":0,"title":["A 32-bp deletion in\n                    <i>LiBBX16<\/i>\n                    underlies the dominant purple leaf trait in crape myrtle"],"prefix":"10.1093","volume":"13","author":[{"given":"Ping","family":"Shen","sequence":"first","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Feng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiufeng","family":"Chi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiting","family":"Wan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qifang","family":"Lin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiqian","family":"Ju","sequence":"additional","affiliation":[{"name":"College of Landscape Architecture and Forestry, Shandong Key Laboratory for Germplasm Innovation of Saline-alkaline Tolerant Grasses and Trees, Qingdao Agricultural University , Qingdao 266109, Shandong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huan","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Radiation Technology, Beijing Academy of Science and Technology , Beijing 1000875 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8612-7659","authenticated-orcid":false,"given":"Tangchun","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Cai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tangren","family":"Cheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-0065","authenticated-orcid":false,"given":"Qixiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0712-3161","authenticated-orcid":false,"given":"Huitang","family":"Pan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University , Beijing 100083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,29]]},"reference":[{"key":"2026092314064469200_ref1","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.pbi.2005.11.003","article-title":"The genetic dissection of floral pollination syndromes","volume":"9","author":"Galliot","year":"2006","journal-title":"Curr Opin Plant 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mechanism underlying the glycosylation and methylation of anthocyanins in peach","volume":"166","author":"Cheng","year":"2014","journal-title":"Plant Physiol"},{"key":"2026092314064469200_ref10","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.foodchem.2018.07.120","article-title":"Anthocyanins accumulation and molecular analysis of correlated genes by metabolome and transcriptome in green and purple asparaguses (Asparagus officinalis L.)","volume":"271","author":"Dong","year":"2019","journal-title":"Food Chem"},{"key":"2026092314064469200_ref11","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1093\/plphys\/kiad160","article-title":"Colorful hues: insight into the mechanisms of anthocyanin pigmentation in fruit","volume":"192","author":"Zhao","year":"2023","journal-title":"Plant Physiol"},{"key":"2026092314064469200_ref12","doi-asserted-by":"crossref","DOI":"10.1016\/j.plaphy.2024.108965","article-title":"AcMYB96 promotes anthocyanin accumulation in onion 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Genet"},{"key":"2026092314064469200_ref28","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1111\/tpj.15877","article-title":"Discovery of a DFR gene that controls anthocyanin accumulation in the spiny Solanum group: roles of a natural promoter variant and alternative splicing","volume":"111","author":"Wang","year":"2022","journal-title":"Plant J"},{"key":"2026092314064469200_ref29","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1007\/s001220050661","article-title":"The retrotransposon RTip1 is integrated into a novel type of minisatellite, MiniSip1, in the genome of the common morning glory and carries another new type of minisatellite, MiniSip2","volume":"95","author":"Hisatomi","year":"1997","journal-title":"Theor Appl Genet"},{"key":"2026092314064469200_ref30","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s12284-024-00713-z","article-title":"OsLSC6 regulates leaf sheath color and cold tolerance in rice revealed by metabolite genome wide 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apples","volume":"21","author":"Espley","year":"2009","journal-title":"Plant Cell"},{"key":"2026092314064469200_ref34","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/s41467-019-09518-x","article-title":"A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour","volume":"10","author":"Zhang","year":"2019","journal-title":"Nat Commun"},{"key":"2026092314064469200_ref35","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1105\/tpc.20.00474","article-title":"Allelic variation of MYB10 is the major force controlling natural variation in skin and flesh color in strawberry (Fragaria spp.) fruit","volume":"32","author":"Castillejo","year":"2020","journal-title":"Plant Cell"},{"key":"2026092314064469200_ref36","doi-asserted-by":"crossref","first-page":"uhae191","DOI":"10.1093\/hr\/uhae191","article-title":"Association analysis of BSA-seq, BSR-seq, and RNA-seq reveals key genes involved in purple leaf formation in a tea population (Camellia sinensis)","volume":"11","author":"Wang","year":"2024","journal-title":"Hortic Res"},{"key":"2026092314064469200_ref37","doi-asserted-by":"crossref","first-page":"101176","DOI":"10.1016\/j.xplc.2024.101176","article-title":"An enhancer-transposable element from purple leaf tea varieties underlies the transition from evergreen to purple leaf color","volume":"6","author":"Xie","year":"2024","journal-title":"Plant Commun"},{"key":"2026092314064469200_ref38","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2024.136300","article-title":"Phenotypic, genetic, variation, and molecular function of CaMYB113 in pepper (Capsicum annuum L.)","volume":"281","author":"Liu","year":"2024","journal-title":"Int J Biol Macromol"},{"key":"2026092314064469200_ref39","doi-asserted-by":"crossref","DOI":"10.1016\/j.xplc.2019.100006","article-title":"Alternative splicing in the anthocyanin fruit gene encoding an R2R3 MYB transcription factor affects anthocyanin biosynthesis in tomato 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