{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:03:18Z","timestamp":1785412998418,"version":"3.56.0"},"reference-count":49,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"publisher","award":["2023YFD2300602"],"award-info":[{"award-number":["2023YFD2300602"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["JIPB"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    The extreme phenotypic diversity in fruit coloration across the\n                    <jats:italic>Citrinae<\/jats:italic>\n                    subtribe poses a fascinating evolutionary puzzle. While carotenoids are essential for plant ecological interactions and human nutrition, the genomic basis underlying their vast metabolic variation in the context of complex species hybridization remains largely elusive. Here, we integrated whole\u2010genome resequencing of 80 representative\n                    <jats:italic>Citrinae<\/jats:italic>\n                    accessions with high\u2010resolution metabolic and transcriptional profiling to elucidate the evolutionary and genetic architectures of citrus fruit coloration. Population genomic modeling demonstrated that pervasive interspecific hybridization and multi\u2010stage introgression from primary progenitors (\n                    <jats:italic>C. reticulata<\/jats:italic>\n                    ,\n                    <jats:italic>C. maxima<\/jats:italic>\n                    , and\n                    <jats:italic>C. medica<\/jats:italic>\n                    ) profoundly reshaped the mosaic metabolic landscapes of modern hybrid taxa (\n                    <jats:italic>C. sinensis<\/jats:italic>\n                    ,\n                    <jats:italic>C. aurantium<\/jats:italic>\n                    , and\n                    <jats:italic>C. limon<\/jats:italic>\n                    ). We uncovered a remarkable tissue\u2010specific decoupling of metabolic flux: CitLCYB2 acts as the primary bottleneck limiting \u03b2\u2010branch flux in the flavedo (peel), coupled with massive CitNCED2\u2010mediated degradation in pummelos, whereas CitPSY1 serves as the core rate\u2010limiting enzyme dictating source\u2010driven accumulation in the pulp. Transgenic validation\n                    <jats:italic>in vivo<\/jats:italic>\n                    using a woody plant callus system directly confirmed the pivotal role of\n                    <jats:italic>CitPSY1<\/jats:italic>\n                    , yielding a &gt;\u200910\u2010fold surge in carotenoid content. Furthermore, by integrating high\u2010resolution local ancestry inference with demography\u2010robust genome\u2010wide scans (CLR, iHS, and XP\u2010CLR), we elucidated the divergent evolutionary trajectories of\n                    <jats:italic>CitPSY1<\/jats:italic>\n                    . We revealed that the ancestral mandarin lineage (\n                    <jats:italic>C. reticulata<\/jats:italic>\n                    ) experienced a strong, targeted regulatory selective sweep to rapidly fix a highly active promoter haplotype for intense pigmentation, whereas pummelos and citrons retained basal metabolic capacities shaped predominantly by natural demographic history. Our findings provide a comprehensive paradigm for how historical gene flow and divergent selection orchestrate secondary metabolism in woody perennials, offering premier genetic targets for the nutritional biofortification of commercial fruits.\n                  <\/jats:p>","DOI":"10.1111\/jipb.70359","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:08:18Z","timestamp":1785409698000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic basis of reticulate evolution and metabolic rewiring driving carotenoid diversity in\n                    <i>Citrinae<\/i>"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-7717-9144","authenticated-orcid":false,"given":"Shunxin","family":"Li","sequence":"first","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4706-0826","authenticated-orcid":false,"given":"Meiling","family":"Yang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7740-2969","authenticated-orcid":false,"given":"Zhongjie","family":"Bu","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1263-7742","authenticated-orcid":false,"given":"Bo","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1111-4809","authenticated-orcid":false,"given":"Zhixin","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1784-3276","authenticated-orcid":false,"given":"Dongqin","family":"Wen","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-9683-2424","authenticated-orcid":false,"given":"Yijing","family":"Ren","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2976-7585","authenticated-orcid":false,"given":"Junli","family":"Ye","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7896-3729","authenticated-orcid":false,"given":"Lijun","family":"Chai","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7971-8565","authenticated-orcid":false,"given":"Zongzhou","family":"Xie","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5852-4315","authenticated-orcid":false,"given":"Xiongjie","family":"Zheng","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4490-4514","authenticated-orcid":false,"given":"Xiuxin","family":"Deng","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation &amp; Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan 430070 China"},{"name":"Hubei Hongshan Laboratory Wuhan 430070 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","first-page":"6939","DOI":"10.1016\/j.cell.2025.08.034","article-title":"Reference genome choice compromises population genetic analyses","volume":"188","author":"Akopyan M.","year":"2025","journal-title":"Cell"},{"key":"e_1_2_9_3_1","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model\u2010based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander D.H.","year":"2009","journal-title":"Genome Res."},{"key":"e_1_2_9_4_1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","article-title":"Major impacts of widespread structural variation on gene expression and crop improvement in tomato","volume":"182","author":"Alonge M.","year":"2020","journal-title":"Cell"},{"key":"e_1_2_9_5_1","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1016\/j.tplants.2021.02.005","article-title":"Domestication of crop metabolomes: Desired and unintended consequences","volume":"26","author":"Alseekh S.","year":"2021","journal-title":"Trends Plant Sci."},{"key":"e_1_2_9_6_1","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two\u2010stage phasing of large\u2010scale sequence data","volume":"108","author":"Browning B.L.","year":"2021","journal-title":"Am. 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