{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T05:14:31Z","timestamp":1790399671510,"version":"4.1.0"},"reference-count":103,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T00:00:00Z","timestamp":1699920000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science and Technology innovation","award":["XZ202301YD0037C"],"award-info":[{"award-number":["XZ202301YD0037C"]}]},{"name":"Economic Forest Seedling Cultivation Project","award":["202375"],"award-info":[{"award-number":["202375"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. 32270685"],"award-info":[{"award-number":["No. 32270685"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Tree peony belongs to one of the Saxifragales families, Paeoniaceae. It is one of the most famous ornamental plants, and is also a promising woody oil plant. Although two Paeoniaceae genomes have been released, their assembly qualities are still to be improved. Additionally, more genomes from wild peonies are needed to accelerate genomic-assisted breeding. Here we assemble a high-quality and chromosome-scale 10.3-Gb genome of a wild Tibetan tree peony, Paeonia ludlowii, which features substantial sequence divergence, including around 75% specific sequences and gene-level differentials compared with other peony genomes. Our phylogenetic analyses suggest that Saxifragales and Vitales are sister taxa and, together with rosids, they are the sister taxon to asterids. The P. ludlowii genome is characterized by frequent chromosome reductions, centromere rearrangements, broadly distributed heterochromatin, and recent continuous bursts of transposable element (TE) movement in peony, although it lacks recent whole-genome duplication. These recent TE bursts appeared during the uplift and glacial period of the Qinghai\u2013Tibet Plateau, perhaps contributing to adaptation to rapid climate changes. Further integrated analyses with methylome data revealed that genome expansion in peony might be dynamically affected by complex interactions among TE proliferation, TE removal, and DNA methylation silencing. Such interactions also impact numerous recently duplicated genes, particularly those related to oil biosynthesis and flower traits. This genome resource will not only provide the genomic basis for tree peony breeding but also shed light on the study of the evolution of huge genome structures as well as their protein-coding genes.<\/jats:p>","DOI":"10.1093\/hr\/uhad241","type":"journal-article","created":{"date-parts":[[2023,11,15]],"date-time":"2023-11-15T00:15:40Z","timestamp":1700007340000},"source":"Crossref","is-referenced-by-count":23,"title":["High-quality assembly and methylome of a Tibetan wild tree peony genome (<i>Paeonia ludlowii)<\/i> reveal the evolution of giant genome architecture"],"prefix":"10.1093","volume":"10","author":[{"given":"Pei-Xuan","family":"Xiao","sequence":"first","affiliation":[{"name":"Huazhong Agricultural University National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, , Wuhan 430070, China"},{"name":"Hubei Hongshan Laboratory, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanrong","family":"Li","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"},{"name":"Tibet Academy of Agricultural and Animal Husbandry Sciences Institute of Vegetables, , Lhasa, Tibet 850002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jin","family":"Lu","sequence":"additional","affiliation":[{"name":"Huazhong Agricultural University National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, , Wuhan 430070, China"},{"name":"Hubei Hongshan Laboratory, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zuo","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gesang","family":"Pingcuo","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"},{"name":"Tibet Academy of Agricultural and Animal Husbandry Sciences Institute of Vegetables, , Lhasa, Tibet 850002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Ying","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"},{"name":"Tibet Academy of Agricultural and Animal Husbandry Sciences Institute of Vegetables, , Lhasa, Tibet 850002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"},{"name":"Tibet Academy of Agricultural and Animal Husbandry Sciences Institute of Vegetables, , Lhasa, Tibet 850002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Xu","sequence":"additional","affiliation":[{"name":"Huazhong Agricultural University National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, , Wuhan 430070, China"},{"name":"Hubei Hongshan Laboratory, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9997-5892","authenticated-orcid":false,"given":"Xiuli","family":"Zeng","sequence":"additional","affiliation":[{"name":"Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China"},{"name":"Tibet Academy of Agricultural and Animal Husbandry Sciences Institute of Vegetables, , Lhasa, Tibet 850002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen-Biao","family":"Jiao","sequence":"additional","affiliation":[{"name":"Huazhong Agricultural University National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, , Wuhan 430070, China"},{"name":"Hubei Hongshan Laboratory, Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,10]]},"reference":[{"key":"2023122807434573100_ref1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/s41438-020-0332-2","article-title":"Germplasm resources and genetic\n\n breeding of Paeonia: a systematic review","volume":"7","author":"Yang","year":"2020","journal-title":"Hortic Res."},{"key":"2023122807434573100_ref2","doi-asserted-by":"crossref","first-page":"uhac079","DOI":"10.1093\/hr\/uhac079","article-title":"Cut peony industry: the first 30 years of research and new horizons","volume":"9","author":"Kamenetsky-Goldstein","year":"2022","journal-title":"Hortic Res."},{"key":"2023122807434573100_ref3","doi-asserted-by":"crossref","first-page":"26944","DOI":"10.1038\/srep26944","article-title":"Fatty acid profile in the seeds and seed tissues of Paeonia L. species as new oil plant resources","volume":"6","author":"Yu","year":"2016","journal-title":"Sci Rep"},{"key":"2023122807434573100_ref4","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41438-019-0194-7","article-title":"Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism","volume":"6","author":"Wang","year":"2019","journal-title":"Hortic Res."},{"key":"2023122807434573100_ref5","doi-asserted-by":"crossref","first-page":"18469","DOI":"10.1038\/s41598-019-54863-y","article-title":"New insights into Paeoniaceae used as medicinal plants in China","volume":"9","author":"Zhang","year":"2019","journal-title":"Sci Rep"},{"key":"2023122807434573100_ref6","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1111\/pbi.13947","article-title":"PoDPBT, a BAHD acyltransferase, catalyses the benzoylation in paeoniflorin biosynthesis in Paeonia ostii","volume":"21","author":"Zhang","year":"2023","journal-title":"Plant Biotechnol J"},{"key":"2023122807434573100_ref7","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1016\/j.phymed.2012.07.013","article-title":"Moutan cortex radicis improves lipopolysaccharide-induced acute lung injury in rats through anti-inflammation","volume":"19","author":"Fu","year":"2012","journal-title":"Phytomedicine"},{"key":"2023122807434573100_ref8","volume-title":"A Study of the Genus Paeonia","author":"Stern","year":"1946"},{"key":"2023122807434573100_ref9","volume-title":"Royal Botanic Gardens","author":"Hong","year":"2010"},{"key":"2023122807434573100_ref10","volume-title":"Royal Botanic 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duplication in plants","volume":"171","author":"Panchy","year":"2016","journal-title":"Plant Physiol"},{"key":"2023122807434573100_ref46","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"2023122807434573100_ref47","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"2023122807434573100_ref48","first-page":"e147","article-title":"Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage","volume":"44","author":"Chakraborty","year":"2016","journal-title":"Nucleic Acids 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Plants."},{"key":"2023122807434573100_ref52","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/j.cels.2018.01.001","article-title":"Juicebox.js provides a cloud-based visualization system for Hi-C data","volume":"6","author":"Robinson","year":"2018","journal-title":"Cell Syst"},{"key":"2023122807434573100_ref53","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2023122807434573100_ref54","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide 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analyses","volume":"25","author":"Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2023122807434573100_ref90","first-page":"15","article-title":"ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees","volume":"19","author":"Zhang","year":"2018","journal-title":"Bioinformatics"},{"key":"2023122807434573100_ref91","doi-asserted-by":"crossref","first-page":"3292","DOI":"10.1093\/molbev\/msaa139","article-title":"ASTRAL-pro: quartet-based species-tree inference despite paralogy","volume":"37","author":"Zhang","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2023122807434573100_ref92","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol Biol 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