{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:21:50Z","timestamp":1787008910885,"version":"build-2736575974"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T00:00:00Z","timestamp":1712620800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Jilin Agricultural University high level researcher grant","award":["JLAUHLRG20102006"],"award-info":[{"award-number":["JLAUHLRG20102006"]}]},{"name":"Promotion Demonstration Project of Forestry Science and Technology of China","award":["JLT2024\u201330"],"award-info":[{"award-number":["JLT2024\u201330"]}]},{"name":"Chinese Key Research and Development Project grant","award":["2019YFC1710700"],"award-info":[{"award-number":["2019YFC1710700"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Saposhnikovia divaricata, 2n\u2009=\u20092x\u2009=\u200916, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia, and other diseases. Here, we assembled a 2.07\u00a0Gb and N50 scaffold length of 227.67\u00a0Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42\u2009948, and 42\u2009456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.<\/jats:p>","DOI":"10.1093\/hr\/uhae105","type":"journal-article","created":{"date-parts":[[2024,4,9]],"date-time":"2024-04-09T08:58:32Z","timestamp":1712653112000},"source":"Crossref","is-referenced-by-count":14,"title":["Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant\n                    <i>Saposhnikovia divaricata<\/i>\n                    (Apiaceae)"],"prefix":"10.1093","volume":"11","author":[{"given":"Zhen-Hui","family":"Wang","sequence":"first","affiliation":[{"name":"Jilin Agricultural University Faculty of Agronomy, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Liu","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Cui","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun-He","family":"Wang","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ze-Liang","family":"Lv","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Cheng","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bao","family":"Liu","sequence":"additional","affiliation":[{"name":"Northeast Normal University Key Laboratory of Molecular Epigenetics of the Ministry of Education, , Changchun 130024, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Liu","sequence":"additional","affiliation":[{"name":"Nanjing Agricultural University State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin-Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University Faculty of Agronomy, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael K","family":"Deyholos","sequence":"additional","affiliation":[{"name":"University of British Columbia Department of Biology, , Okanagan V1V1V7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhong-Ming","family":"Han","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Min","family":"Yang","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University College of Chinese Medicinal Materials, , Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7900-5001","authenticated-orcid":false,"given":"Ai-Sheng","family":"Xiong","sequence":"additional","affiliation":[{"name":"Nanjing Agricultural University State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1507-4718","authenticated-orcid":false,"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"Jilin Agricultural University Faculty of Agronomy, , Changchun 130118, China"},{"name":"University of British Columbia Department of Biology, , Okanagan V1V1V7, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,4,9]]},"reference":[{"key":"2024062609462212500_ref1","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1007\/s11655-020-3091-x","article-title":"Saposhnikovia divaricata \u2013 an ethnopharmacological, phytochemical and pharmacological review","volume":"26","author":"Yang","year":"2020","journal-title":"Chin J Integr Med."},{"key":"2024062609462212500_ref2","first-page":"255","article-title":"Saposhnikovia divaricata: a phytochemical, pharmacological, and pharmacokinetic review","volume":"15","author":"Kreiner","year":"2017","journal-title":"Chin J Nat Med."},{"key":"2024062609462212500_ref3","first-page":"156","volume-title":"Pharmacopoeia of the People's Republic of China","author":"National Pharmacopoeia Committee","year":"2020"},{"key":"2024062609462212500_ref4","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1186\/s12864-022-08821-0","article-title":"Comparative analysis of the chloroplast and mitochondrial genomes of Saposhnikovia divaricata revealed the possible transfer of plastome repeat regions into the mitogenome","volume":"23","author":"Ni","year":"2022","journal-title":"BMC Genomics."},{"key":"2024062609462212500_ref5","doi-asserted-by":"crossref","first-page":"931","DOI":"10.3390\/genes13050931","article-title":"The chloroplast genome of wild Saposhnikovia divaricata: genomic features, comparative analysis, and phylogenetic relationships","volume":"13","author":"Yi","year":"2022","journal-title":"Genes (Basel)."},{"key":"2024062609462212500_ref6","doi-asserted-by":"crossref","first-page":"4651","DOI":"10.1016\/j.tet.2015.04.092","article-title":"Three new coumarins from Saposhnikovia divaricata and their porcine epidemic diarrhea virus (PEDV) inhibitory activity","volume":"71","author":"Yang","year":"2015","journal-title":"Tetrahedron."},{"key":"2024062609462212500_ref7","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1007\/s11418-020-01430-9","article-title":"Characterization of metabolites in Saposhnikovia divaricata root from Mongolia","volume":"75","author":"Batsukh","year":"2021","journal-title":"J Nat Med."},{"key":"2024062609462212500_ref8","first-page":"227","article-title":"Anti-proliferative and antioxidant activities of Saposhnikovia divaricata","volume":"18","author":"Tai","year":"2007","journal-title":"Oncol Rep."},{"key":"2024062609462212500_ref9","doi-asserted-by":"crossref","first-page":"1984238","DOI":"10.1155\/2016\/1984238","article-title":"Anti-inflammatory and antiosteoarthritis effects of Saposhnikovia divaricata ethanol extract: In vitro and in vivo studies","author":"Chun","year":"2016","journal-title":"Evid Based Complement Alternat Med."},{"key":"2024062609462212500_ref10","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1248\/cpb.49.154","article-title":"Analgesic components of saposhnikovia root (Saposhnikovia divaricata)","volume":"49","author":"Okuyama","year":"2001","journal-title":"Chem Pharm Bull (Tokyo)."},{"key":"2024062609462212500_ref11","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1016\/j.phymed.2015.09.002","article-title":"Radix Saposhnikovia extract suppresses mouse allergic contact dermatitis by regulating dendritic-cell-activated Th1 cells","volume":"22","author":"Yu","year":"2015","journal-title":"Phytomedicine."},{"key":"2024062609462212500_ref12","first-page":"1569","article-title":"Chemical constituents of roots of Saposhnikovia divaricata","volume":"35","author":"Zhao","year":"2010","journal-title":"Zhongguo Zhong Yao Za Zhi."},{"key":"2024062609462212500_ref13","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1016\/j.jep.2013.05.023","article-title":"The suppressive effects of Saposhnikovia divaricata (Fangfeng) chromone extract on rheumatoid arthritis via inhibition of nuclear factor-\u03baB and mitogen activated proteinkinases activation on collagen-induced arthritis model","volume":"148","author":"Kong","year":"2013","journal-title":"J Ethnopharmacol."},{"key":"2024062609462212500_ref14","doi-asserted-by":"crossref","first-page":"2926","DOI":"10.1111\/jcmm.13204","article-title":"Cimifugin suppresses allergic inflammation by reducing epithelial derived initiative key factors via regulating tight junctions","volume":"21","author":"Wang","year":"2017","journal-title":"J Cell Mol Med."},{"key":"2024062609462212500_ref15","first-page":"264","article-title":"Isolation, identification and biocontrol potential of rhizospheric fungus of Saposhnikovia divaricata","volume":"39","author":"Sun","year":"2023","journal-title":"Biotechnol Bull."},{"key":"2024062609462212500_ref16","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.3390\/agronomy12112906","article-title":"Effect of rhizospheric fungus on biological control of root rot (Fusarium equiseti) disease of Saposhnikovia divaricata","volume":"12","author":"Han","year":"2022","journal-title":"Agronomy."},{"key":"2024062609462212500_ref17","first-page":"59","article-title":"Effects of different phosphorus concentrations on soil physicochemical property, growth and medicinal materials quality of Saposhnikovia divaricata","volume":"43","author":"Hao","year":"2022","journal-title":"J South China Agric Univ."},{"key":"2024062609462212500_ref18","first-page":"446","article-title":"Transcriptomic analysis identifies differentially expressed genes (DEGs) associated with bolting and flowering in Saposhnikovia divaricata","volume":"16","author":"Liu","year":"2018","journal-title":"Chin J Nat Med."},{"key":"2024062609462212500_ref19","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s11418-016-0969-1","article-title":"Comparative analysis of the constituents in Saposhnikoviae Radix and Glehniae Radix cum Rhizoma by monitoring inhibitory activity of nitric oxide production","volume":"70","author":"Kamino","year":"2016","journal-title":"J Nat Med."},{"key":"2024062609462212500_ref20","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.2135\/cropsci2019.05.0333","article-title":"Distributions and conservation status of carrot wild relatives in Tunisia: a case study in the western Mediterranean basin","volume":"59","author":"Mezghani","year":"2019","journal-title":"Crop 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characteristics","volume":"10","author":"Fu","year":"2022","journal-title":"Hortic Res."},{"key":"2024062609462212500_ref31","doi-asserted-by":"crossref","first-page":"uhac241","DOI":"10.1093\/hr\/uhac241","article-title":"Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color","volume":"10","author":"Nie","year":"2022","journal-title":"Hortic Res."},{"key":"2024062609462212500_ref32","doi-asserted-by":"crossref","first-page":"uhad103","DOI":"10.1093\/hr\/uhad103","article-title":"Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics","volume":"10","author":"Wang","year":"2023","journal-title":"Hortic Res."},{"key":"2024062609462212500_ref33","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1038\/ng.695","article-title":"Genome-wide association studies of 14 agronomic traits in rice landraces","volume":"42","author":"Huang","year":"2010","journal-title":"Nat 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Schischk","volume":"29","author":"Gao","year":"2023","journal-title":"Chin J Integr Med."},{"key":"2024062609462212500_ref41","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1101\/gr.5290206","article-title":"Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice","volume":"16","author":"Piegu","year":"2006","journal-title":"Genome Res."},{"key":"2024062609462212500_ref42","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1093\/gbe\/evt025","article-title":"Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution","volume":"5","author":"El Baidouri","year":"2013","journal-title":"Genome Biol Evol."},{"key":"2024062609462212500_ref43","doi-asserted-by":"crossref","first-page":"378","DOI":"10.4103\/pm.pm_323_16","article-title":"Prim-O-glucosylcimifugin attenuates lipopolysaccharide induced inflammatory response in RAW 264.7 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the prediction of full-length LTR retrotransposons","volume":"35","author":"Zhao","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2024062609462212500_ref47","doi-asserted-by":"crossref","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","article-title":"De novo identification of repeat families in large genomes","volume":"21","author":"Price","year":"2005","journal-title":"Bioinformatics."},{"key":"2024062609462212500_ref48","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr Protoc Bioinformatics."},{"key":"2024062609462212500_ref49","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell 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phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics."},{"key":"2024062609462212500_ref53","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1093\/molbev\/mst100","article-title":"Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3","volume":"30","author":"Han","year":"2013","journal-title":"Mol Biol Evol."},{"key":"2024062609462212500_ref54","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024062609462212500_ref55","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1107s32","article-title":"Aligning short sequencing reads with Bowtie","author":"Langmead","year":"2010","journal-title":"Curr Protoc 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