{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T16:48:18Z","timestamp":1774543698142,"version":"3.50.1"},"reference-count":123,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T00:00:00Z","timestamp":1733961600000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The genomic basis and biology of winged fruit are interesting issues in ecological and evolutionary biology. Chinese wingnut (Pterocarya stenoptera) is an important horticultural and economic tree species in China. The genomic resources of this hardwood tree could advance the genomic studies of Juglandaceae species and elucidate their evolutionary relationships. Here, we reported a high-quality reference genome of P. stenoptera (N50 = 35.15 Mb) and performed a comparative genomic analysis across Juglandaceae species. Paralogous relationships among the 16 chromosomes of P. stenoptera revealed eight main duplications representing the subgenomes. Molecular dating suggested that the most recent common ancestor of P. stenoptera and Cyclocarya paliurus diverged from Juglans species around 56.7 million years ago (MYA). The expanded and contracted gene families were associated with cutin, suberine, and wax biosynthesis, cytochrome P450, and anthocyanin biosynthesis. We identified large inversion blocks between P. stenoptera and its relatives, which were enriched with genes involved in lipid biosynthesis and metabolism, as well as starch and sucrose metabolism. Whole-genome resequencing of 28 individuals revealed clearly phylogenetic clustering into three groups corresponding to Pterocarya macroptera, Pterocarya hupehensis, and P. stenoptera. Morphological and transcriptomic analyses showed that CAD, COMT, LOX, and MADS-box play important roles during the five developmental stages of wingnuts. This study highlights the evolutionary history of the P. stenoptera genome and supports P. stenoptera as an appropriate Juglandaceae model for studying winged fruits. Our findings provide a theoretical basis for understanding the evolution, development, and diversity of winged fruits in woody plants.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae087","type":"journal-article","created":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T21:20:49Z","timestamp":1734038449000},"source":"Crossref","is-referenced-by-count":4,"title":["Genome Assembly and Winged Fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7054-5749","authenticated-orcid":false,"given":"Fangdong","family":"Geng","sequence":"first","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]},{"name":"Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8273-5798","authenticated-orcid":false,"given":"Xuedong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]},{"name":"Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6452-2998","authenticated-orcid":false,"given":"Jiayu","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-6414-5937","authenticated-orcid":false,"given":"Hengzhao","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4507-8480","authenticated-orcid":false,"given":"Hang","family":"Ye","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2086-3347","authenticated-orcid":false,"given":"Fan","family":"Hao","sequence":"additional","affiliation":[{"name":"College of Forestry, Northwest A&F University , Yangling 712100,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9628-2113","authenticated-orcid":false,"given":"Miaoqing","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3836-6574","authenticated-orcid":false,"given":"Meng","family":"Dang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-1611-2377","authenticated-orcid":false,"given":"Huijuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Xi\u2019an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province , Xi\u2019an 710061,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5526-9670","authenticated-orcid":false,"given":"Mengdi","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3033-6982","authenticated-orcid":false,"given":"Peng","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University , Xi\u2019an 710069,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2024,12,12]]},"reference":[{"key":"2025043019534818600_qzae087-B1","first-page":"396","article-title":"Evolution of fruit types and seed dispersal: a phylogenetic and ecological 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Ecol Evol"},{"key":"2025043019534818600_qzae087-B4","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1007\/s12229-011-9093-9","article-title":"A comparison of frugivory and scatter-hoarding seed-dispersal syndromes","volume":"78","author":"Vander","year":"2011","journal-title":"Bot Rev"},{"key":"2025043019534818600_qzae087-B5","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.ppees.2014.03.001","article-title":"Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene","volume":"16","author":"Xiang","year":"2014","journal-title":"Perspect Plant Ecol Evol Syst"},{"key":"2025043019534818600_qzae087-B6","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1111\/brv.12164","article-title":"Evolution of angiosperm seed disperser mutualisms: the timing of origins and their consequences for coevolutionary interactions between angiosperms and frugivores","volume":"91","author":"Eriksson","year":"2016","journal-title":"Biol Rev Camb Philos Soc"},{"key":"2025043019534818600_qzae087-B7","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1086\/303367","article-title":"Seed size, fruit size, and dispersal systems in angiosperms from the Early Cretaceous to the Late Tertiary","volume":"156","author":"Eriksson","year":"2000","journal-title":"Am Nat"},{"key":"2025043019534818600_qzae087-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s12229-010-9041-0","article-title":"Phylogenetic distribution and identification of fin-winged fruits","volume":"76","author":"Manchester","year":"2010","journal-title":"Bot Rev"},{"key":"2025043019534818600_qzae087-B9","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1111\/jse.12808","article-title":"Loss of innovative traits underlies multiple origins of Aquilegia ecalcarata","volume":"60","author":"Geng","year":"2022","journal-title":"J Syst Evol"},{"key":"2025043019534818600_qzae087-B10","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1007\/s11099-015-0171-9","article-title":"Photosynthesis and growth adaptation of Pterocarya stenoptera and Pinus elliottii seedlings to submergence and drought","volume":"54","author":"Yang","year":"2016","journal-title":"Photosynthetica"},{"key":"2025043019534818600_qzae087-B11","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1111\/jse.12699","article-title":"Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut (Pterocarya stenoptera)","volume":"60","author":"Li","year":"2022","journal-title":"J Syst Evol"},{"key":"2025043019534818600_qzae087-B12","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1016\/j.ygeno.2021.06.005","article-title":"Physiological and transcriptional changes provide insights into the effect of root waterlogging on the aboveground part of Pterocarya stenoptera","volume":"113","author":"Li","year":"2021","journal-title":"Genomics"},{"key":"2025043019534818600_qzae087-B13","doi-asserted-by":"crossref","first-page":"4828","DOI":"10.1002\/ece3.6236","article-title":"Shifts in potential geographical distribution of Pterocarya stenoptera under climate change scenarios in China","volume":"10","author":"Zhang","year":"2020","journal-title":"Ecol Evol"},{"key":"2025043019534818600_qzae087-B14","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1016\/j.ygeno.2020.09.027","article-title":"Physiological analysis and transcriptome sequencing reveal the effects of drier air humidity stress on Pterocarya stenoptera","volume":"112","author":"Ye","year":"2020","journal-title":"Genomics"},{"key":"2025043019534818600_qzae087-B15","doi-asserted-by":"crossref","first-page":"3719","DOI":"10.1038\/s41467-020-17498-6","article-title":"Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea 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fruit ripeness and ester formation","volume":"23","author":"Huang","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025043019534818600_qzae087-B46","doi-asserted-by":"crossref","first-page":"108271","DOI":"10.1016\/j.plaphy.2023.108271","article-title":"Identification, characterization, and expression of lipoxygenase genes in sweet cherry (Prunus avium L.) cv. Regina and their relationship with the development of an herbaceous off-flavor during fruit ripening","volume":"206","author":"Villavicencio","year":"2024","journal-title":"Plant Physiol Biochem"},{"key":"2025043019534818600_qzae087-B47","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1360\/N052018-00225","article-title":"Evolutionary developmental mechanisms underlying the origin and diversification of the fruits","volume":"49","author":"He","year":"2019","journal-title":"Sci Sin Vitae"},{"key":"2025043019534818600_qzae087-B48","doi-asserted-by":"crossref","first-page":"4869","DOI":"10.1093\/jxb\/erx303","article-title":"Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits","volume":"68","author":"Huang","year":"2017","journal-title":"J Exp Bot"},{"key":"2025043019534818600_qzae087-B49","doi-asserted-by":"crossref","first-page":"3485","DOI":"10.1105\/tpc.19.00695","article-title":"Auxin regulates sucrose 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evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan","volume":"2","author":"Xiao","year":"2021","journal-title":"Plant Commun"},{"key":"2025043019534818600_qzae087-B53","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/sysbio\/syab030","article-title":"Fossil-informed models reveal a boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae)","volume":"71","author":"Zhang","year":"2021","journal-title":"Syst Biol"},{"key":"2025043019534818600_qzae087-B54","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/s12862-021-01917-3","article-title":"Whole genome based insights into the phylogeny and evolution of the Juglandaceae","volume":"21","author":"Zhou","year":"2021","journal-title":"BMC Ecol Evol"},{"key":"2025043019534818600_qzae087-B55","doi-asserted-by":"crossref","first-page":"100497","DOI":"10.1016\/j.xplc.2022.100497","article-title":"Pistachio genomes provide insights into 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