[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"detail-sidebar-cat-0-en-105":3,"doc-detail-156178-en":59,"doc-seo-156178-105":82},{"code":4,"msg":5,"data":6},0,"success",[7,13,18,23,28,33,38,43,48,51,55],{"id":8,"doc_module":4,"doc_module_name":9,"category_name":10,"show_sort_weight":11,"slug":12},1,"Document","Story & Novel",90,"story-novel",{"id":14,"doc_module":4,"doc_module_name":9,"category_name":15,"show_sort_weight":16,"slug":17},2,"Literature",80,"literature",{"id":19,"doc_module":4,"doc_module_name":9,"category_name":20,"show_sort_weight":21,"slug":22},4,"Exam",70,"exam",{"id":24,"doc_module":4,"doc_module_name":9,"category_name":25,"show_sort_weight":26,"slug":27},5,"Comic",60,"comic",{"id":29,"doc_module":4,"doc_module_name":9,"category_name":30,"show_sort_weight":31,"slug":32},6,"Technology",50,"technology",{"id":34,"doc_module":4,"doc_module_name":9,"category_name":35,"show_sort_weight":36,"slug":37},7,"Healthcare",40,"healthcare",{"id":39,"doc_module":4,"doc_module_name":9,"category_name":40,"show_sort_weight":41,"slug":42},8,"Research & Report",30,"research-report",{"id":44,"doc_module":4,"doc_module_name":9,"category_name":45,"show_sort_weight":46,"slug":47},9,"Religion & Spirituality",20,"religion-spirituality",{"id":46,"doc_module":4,"doc_module_name":9,"category_name":49,"show_sort_weight":46,"slug":50},"World Cup","world-cup",{"id":52,"doc_module":4,"doc_module_name":9,"category_name":53,"show_sort_weight":52,"slug":54},10,"Lifestyle","lifestyle",{"id":56,"doc_module":4,"doc_module_name":9,"category_name":57,"show_sort_weight":24,"slug":58},19,"General","general",{"code":4,"msg":5,"data":60},{"doc_id":61,"user_id":62,"nickname":63,"user_avatar":64,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":66,"doc_content":67,"file_id":68,"file_url":69,"file_type":70,"file_size":71,"view_count":72,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":73,"language":74,"language_code":75,"site_id":76,"html_lang":75,"table_of_contents":77,"faqs":78,"seo_title":79,"seo_description":66,"update_tm":80,"read_time":81,"preview_page_count":4},156178,13056703019662,"Evangeline","https://ap-avatar.wpscdn.com/avatar/be000253a8e92610077?_k=1778726343310543188","Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants","Plant specialized metabolites enhance environmental fitness, exemplified by caffeine and crocins, two compound classes found in distantly related genera that likely arose via convergent evolution. The study reports a chromosomal-level genome assembly of Gardenia jasminoides and fully resolves the dedicated crocin biosynthesis pathway using genomic and functional assays. Comparative analyses with Coffea canephora and other eudicot genomes show independent, recent tandem duplications for Coffea caffeine synthases and GjCCD4a, while later Gardenia pathway genes evolved through older duplications and were recruited after GjCCD4a.","Xu et al. BMC Biology (2020) 18:63 [https://doi.org/10.1186/s12915-020-00795-3](https://doi.org/10.1186/s12915-020-00795-3)  \nRESEARCH ARTICLE Open Access   \nTandem gene duplications drive divergent evolution of caffeine and crocin  \nbiosynthetic pathways in plants  \nZhichao Xu 1,2†, Xiangdong Pu 1†, Ranran Gao 1, Olivia Costantina Demurtas3, Steven J. Fleck4, Michaela Richter4, Chunnian He 1,2, Aijia Ji 1, Wei Sun5, Jianqiang Kong6, Kaizhi Hu7, Fengming Ren 1,7, Jiejie Song8, Zhe Wang6, Ting Gao8, Chao Xiong5, Haoying Yu 1, Tianyi Xin 1, Victor A. Albert4,9, Giovanni Giuliano3*, Shilin Chen2,5* and Jingyuan Song 1,2,10*  \nAbstract  \nBackground: Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of compounds are found in a handful of distantly related plant genera (Coffea, Camellia, Paullinia, and Ilex for caffeine; Crocus, Buddleja, and Gardenia for crocins) wherein they presumably evolved through convergent evolution. The closely related Coffea and Gardenia genera belong to the Rubiaceae family and synthesize, respectively, caffeine and crocins in their fruits.  \nResults: Here, we report a chromosomal-level genome assembly of Gardenia jasminoides, a crocin-producing species, obtained using Oxford Nanopore sequencing and Hi-C technology. Through genomic and functional assays, we completely deciphered for the first time in any plant the dedicated pathway of crocin biosynthesis. Through comparative analyses with Coffea canephora and other eudicot genomes, we show that Coffea caffeine synthases and the first dedicated gene in the Gardenia crocin pathway, GjCCD4a, evolved through recent tandem gene duplications in the two different genera, respectively. In contrast, genes encoding later steps of the Gardenia crocin pathway, ALDH and UGT, evolved through more ancient gene duplications and were presumably recruited into the crocin biosynthetic pathway only after the evolution of the GjCCD4a gene.  \n(Continued on next page)  \n* Correspondence: [giovanni.giuliano@enea.it](giovanni.giuliano@enea.it); [slchen@icmm.ac.cn](slchen@icmm.ac.cn); [jysong@implad.ac.cn](jysong@implad.ac.cn)  \n†Zhichao Xu and Xiangdong Pu contributed equally to this work.  \n3Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Res. Ctr, 00123 Rome, Italy 2Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China  \n1Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China  \nFull list of author information is available at the end of the article  \n© The Author(s) . 2020 Open Access This article is licensed under a Creative Commons Attribution 4 . 0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit [http://creativecommons.org/licenses/by/4.0/](http://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver ([http://creativecommons.org/publicdomain/zero/1.0/](http://creativecommo","cbCaislTfNE0vFj4","https://ap.wps.com/l/cbCaislTfNE0vFj4","pdf",1754693,11,14,"English","en",105,"# Abstract\n## Background\n## Results\n## Conclusions\n# Keywords\n# Background","[{\"question\":\"What evolutionary process links caffeine and crocin pathway divergence in this study?\",\"answer\":\"The study shows that tandem gene duplications contributed to divergent evolution of caffeine and crocin biosynthetic pathways in different plant genera.\"},{\"question\":\"What genome resource was generated for Gardenia jasminoides?\",\"answer\":\"A chromosomal-level genome assembly of Gardenia jasminoides was produced using Oxford Nanopore sequencing and Hi-C technology.\"},{\"question\":\"How did gene duplication timing differ across the Gardenia crocin pathway?\",\"answer\":\"Genes for later steps (ALDH and UGT) reflect more ancient duplications, while the first dedicated crocin pathway gene GjCCD4a evolved through recent tandem gene duplications.\"}]","Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants | PDF",1787954707,35,{"code":4,"msg":83,"data":84},"ok",{"site_id":76,"language":75,"slug":85,"title":65,"keywords":86,"description":66,"schema_data":87,"social_meta":141,"head_meta":143,"extra_data":145,"updated_unix":80},"tandem-gene-duplications-drive-divergent-evolution-of-caffeine-and-crocin-biosynthetic-pathways-in-plants","",{"@graph":88,"@context":140},[89,103,123],{"@type":90,"itemListElement":91},"BreadcrumbList",[92,96,98,101],{"item":93,"name":94,"@type":95,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":97,"name":9,"@type":95,"position":14},"https://docshare.wps.com/document/",{"item":99,"name":40,"@type":95,"position":100},"https://docshare.wps.com/document/research-report/",3,{"item":102,"name":65,"@type":95,"position":19},"https://docshare.wps.com/document/tandem-gene-duplications-drive-divergent-evolution-of-caffeine-and-crocin-biosynthetic-pathways-in-plants/156178/",{"url":102,"name":65,"@type":104,"image":105,"author":110,"headline":65,"publisher":112,"fileFormat":115,"inLanguage":75,"description":66,"dateModified":116,"datePublished":117,"encodingFormat":115,"isAccessibleForFree":118,"interactionStatistic":119},"DigitalDocument",{"url":106,"@type":107,"width":108,"height":109},"https://docshare.wps.com/thumbnails/tandem-gene-duplications-drive-divergent-evolution-of-caffeine-and-crocin-biosynthetic-pathways-in-plants/156178.png","ImageObject",300,407,{"name":63,"@type":111},"Person",{"url":93,"name":113,"@type":114},"DocShare","Organization","application/pdf","2026-11-09","2026-08-28",true,{"@type":120,"interactionType":121,"userInteractionCount":72},"InteractionCounter",{"@type":122},"ViewAction",{"@type":124,"mainEntity":125},"FAQPage",[126,132,136],{"name":127,"@type":128,"acceptedAnswer":129},"What evolutionary process links caffeine and crocin pathway divergence in this study?","Question",{"text":130,"@type":131},"The study shows that tandem gene duplications contributed to divergent evolution of caffeine and crocin biosynthetic pathways in different plant genera.","Answer",{"name":133,"@type":128,"acceptedAnswer":134},"What genome resource was generated for Gardenia jasminoides?",{"text":135,"@type":131},"A chromosomal-level genome assembly of Gardenia jasminoides was produced using Oxford Nanopore sequencing and Hi-C technology.",{"name":137,"@type":128,"acceptedAnswer":138},"How did gene duplication timing differ across the Gardenia crocin pathway?",{"text":139,"@type":131},"Genes for later steps (ALDH and UGT) reflect more ancient duplications, while the first dedicated crocin pathway gene GjCCD4a evolved through recent tandem gene duplications.","https://schema.org",{"og:url":102,"og:type":142,"og:title":65,"og:site_name":113,"og:description":66},"article",{"robots":144,"canonical":102},"index,follow",{"doc_id":61,"site_id":76}]