{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T02:42:25Z","timestamp":1793155345438,"version":"4.5.0"},"reference-count":112,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T00:00:00Z","timestamp":1743724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T00:00:00Z","timestamp":1743724800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat. Plants"],"DOI":"10.1038\/s41477-025-01955-5","type":"journal-article","created":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T23:36:36Z","timestamp":1743809796000},"page":"775-789","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3604-6468","authenticated-orcid":false,"given":"Bixuan","family":"Cheng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0468-2128","authenticated-orcid":false,"given":"Kai","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7122-2522","authenticated-orcid":false,"given":"Meichun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0665-6508","authenticated-orcid":false,"given":"Peter M.","family":"Bourke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1857-4841","authenticated-orcid":false,"given":"Lijun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1824-2798","authenticated-orcid":false,"given":"Sihui","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanlin","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lifang","family":"Geng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8192-3186","authenticated-orcid":false,"given":"Wenting","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8008-099X","authenticated-orcid":false,"given":"Chenyang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juntong","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runhuan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4207-2307","authenticated-orcid":false,"given":"Xiaoling","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"He","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huitang","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-0065","authenticated-orcid":false,"given":"Qixiang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8143-1931","authenticated-orcid":false,"given":"Le","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8096-5333","authenticated-orcid":false,"given":"Chao","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,4,4]]},"reference":[{"key":"1955_CR1","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.tplants.2021.09.004","volume":"27","author":"A Altman","year":"2022","unstructured":"Altman, A., Shennan, S. & Odling-Smee, J. Ornamental plant domestication by aesthetics-driven human cultural niche construction. Trends Plant Sci. 27, 124\u2013138 (2022).","journal-title":"Trends Plant Sci."},{"key":"1955_CR2","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.2135\/cropsci2016.10.0885","volume":"57","author":"H Dempewolf","year":"2017","unstructured":"Dempewolf, H. et al. Past and future use of wild relatives in crop breeding. Crop Sci. 57, 1070\u20131082 (2017).","journal-title":"Crop Sci."},{"key":"1955_CR3","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/s41586-024-07682-9","volume":"632","author":"S Cheng","year":"2024","unstructured":"Cheng, S. et al. Harnessing landrace diversity empowers wheat breeding. Nature 632, 823\u2013831 (2024).","journal-title":"Nature"},{"key":"1955_CR4","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1016\/j.tibtech.2021.08.009","volume":"40","author":"A Bohra","year":"2022","unstructured":"Bohra, A. et al. Reap the crop wild relatives for breeding future crops. Trends Biotechnol. 40, 412\u2013431 (2022).","journal-title":"Trends Biotechnol."},{"key":"1955_CR5","doi-asserted-by":"crossref","unstructured":"Smulders, M. J. M., et al. In Wild Crop Relatives: Genomic and Breeding Resources: Plantation and Ornamental Crops (ed. Kole, C.) 243\u2013275 (Springer, 2011).","DOI":"10.1007\/978-3-642-21201-7_12"},{"key":"1955_CR6","unstructured":"Kr\u00fcssmann, G. The Complete Book of Roses (Timber, 1981)."},{"key":"1955_CR7","doi-asserted-by":"publisher","unstructured":"Thibault, L., et al. Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics. Preprint at bioRxiv, https:\/\/doi.org\/10.1101\/2023.06.22.546162 (2024).","DOI":"10.1101\/2023.06.22.546162"},{"key":"1955_CR8","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1016\/j.tree.2022.04.006","volume":"37","author":"MD Purugganan","year":"2022","unstructured":"Purugganan, M. D. What is domestication? Trends Ecol. Evol. 37, 663\u2013671 (2022).","journal-title":"Trends Ecol. Evol."},{"key":"1955_CR9","first-page":"555","volume":"79","author":"A Wyile","year":"1954","unstructured":"Wyile, A. The history of garden roses. Part I. J. Roy. Hort. Soc. 79, 555\u2013571 (1954).","journal-title":"J. Roy. Hort. Soc."},{"key":"1955_CR10","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1038\/s41588-018-0110-3","volume":"50","author":"O Raymond","year":"2018","unstructured":"Raymond, O. et al. The Rosa genome provides new insights into the domestication of modern roses. Nat. Genet. 50, 772\u2013777 (2018).","journal-title":"Nat. Genet."},{"key":"1955_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-15815-6","volume":"7","author":"J Tan","year":"2017","unstructured":"Tan, J. et al. Genetic relationships and evolution of old Chinese garden roses based on SSRs and chromosome diversity. Sci. Rep. 7, 15437 (2017).","journal-title":"Sci. Rep."},{"key":"1955_CR12","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.scienta.2013.08.015","volume":"162","author":"M Vukosavljev","year":"2013","unstructured":"Vukosavljev, M. et al. Genetic diversity and differentiation in roses: a garden rose perspective. Sci. Hortic. 162, 320\u2013332 (2013).","journal-title":"Sci. Hortic."},{"key":"1955_CR13","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/S0304-4238(98)00169-1","volume":"77","author":"S Matsumoto","year":"1998","unstructured":"Matsumoto, S. et al. Phylogenetic analyses of the genus Rosa using the matK sequence: molecular evidence for the narrow genetic background of modern roses. Sci. Hortic. 77, 73\u201382 (1998).","journal-title":"Sci. Hortic."},{"key":"1955_CR14","doi-asserted-by":"publisher","first-page":"353","DOI":"10.3732\/ajb.95.3.353","volume":"95","author":"WJM Koopman","year":"2008","unstructured":"Koopman, W. J. M. et al. AFLP markers as a tool to reconstruct complex relationships: a case study in Rosa (Rosaceae). Am. J. Bot. 95, 353\u2013366 (2008).","journal-title":"Am. J. Bot."},{"key":"1955_CR15","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1093\/aob\/mcu245","volume":"115","author":"M Fougere-Danezan","year":"2015","unstructured":"Fougere-Danezan, M., Joly, S., Bruneau, A., Gao, X. F. & Zhang, L. B. Phylogeny and biogeography of wild roses with specific attention to polyploids. Ann. Bot. 115, 275\u2013291 (2015).","journal-title":"Ann. Bot."},{"key":"1955_CR16","unstructured":"Luo, L. Genus Rosa L. in China (China Forestry Publishing House, 2024)."},{"key":"1955_CR17","doi-asserted-by":"crossref","unstructured":"Rehder, A. Bibliography of Cultivated Trees and Shrubs Hardy in the Cooler Temperate Regions of the Northern Hemisphere (Arnold Arboretum of Harvard University, 1949).","DOI":"10.5962\/bhl.title.60035"},{"key":"1955_CR18","unstructured":"Wissemann, V. Reference Module in Life Sciences (Elsevier, 2017)."},{"key":"1955_CR19","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1111\/j.1095-8339.2005.00368.x","volume":"147","author":"V Wissemann","year":"2005","unstructured":"Wissemann, V. & Ritz, C. M. The genus Rosa (Rosoideae, Rosaceae) revisited: molecular analysis of nrITS-1 and atp B-rbc L intergenic spacer (IGS) versus conventional taxonomy. Bot. J. Linn. Soc. 147, 275\u2013290 (2005).","journal-title":"Bot. J. Linn. Soc."},{"key":"1955_CR20","doi-asserted-by":"publisher","first-page":"1659","DOI":"10.1038\/s41477-024-01820-x","volume":"10","author":"Z Zhang","year":"2024","unstructured":"Zhang, Z. et al. Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose. Nat. Plants 10, 1659\u20131671 (2024).","journal-title":"Nat. Plants"},{"key":"1955_CR21","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s43897-024-00088-1","volume":"4","author":"X Zhang","year":"2024","unstructured":"Zhang, X. et al. Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits. Mol. Hortic. 4, 14 (2024).","journal-title":"Mol. Hortic."},{"key":"1955_CR22","doi-asserted-by":"publisher","first-page":"nwab092","DOI":"10.1093\/nsr\/nwab092","volume":"8","author":"M Zhong","year":"2021","unstructured":"Zhong, M. et al. Rose without prickle: genomic insights linked to moisture adaptation. Natl Sci. Rev. 8, nwab092 (2021).","journal-title":"Natl Sci. Rev."},{"key":"1955_CR23","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/s41438-021-00594-z","volume":"8","author":"F Chen","year":"2021","unstructured":"Chen, F. et al. A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. Hortic. Res. 8, 141 (2021).","journal-title":"Hortic. Res."},{"key":"1955_CR24","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41477-018-0166-1","volume":"4","author":"L Hibrand Saint-Oyant","year":"2018","unstructured":"Hibrand Saint-Oyant, L. et al. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat. Plants 4, 473\u2013484 (2018).","journal-title":"Nat. Plants"},{"key":"1955_CR25","unstructured":"Ku, T. R. K. Rosa (Rosaceae). In Flora of China 9 (eds Wu, Z.Y. & Raven, P.H.) (Missouri Botanical Garden, 2003)."},{"key":"1955_CR26","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1134\/S106235902360469X","volume":"51","author":"IA Schanzer","year":"2024","unstructured":"Schanzer, I. A., Fedorova, A. V. & Meschersky, I. G. A haplotype network approach to reconstruct the phylogeny of Rosa L. (Rosaceae). Biol. Bull. 51, 331\u2013345 (2024).","journal-title":"Biol. Bull."},{"key":"1955_CR27","doi-asserted-by":"publisher","first-page":"uhad127","DOI":"10.1093\/hr\/uhad127","volume":"10","author":"YZ Lin","year":"2023","unstructured":"Lin, Y. Z. et al. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic. Res. 10, uhad127 (2023).","journal-title":"Hortic. Res."},{"key":"1955_CR28","doi-asserted-by":"publisher","first-page":"15004","DOI":"10.1038\/nplants.2015.4","volume":"1","author":"NM Springer","year":"2015","unstructured":"Springer, N. M. Transposable elements: microbiomes in the genomes. Nat. Plants 1, 15004 (2015).","journal-title":"Nat. Plants"},{"key":"1955_CR29","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1146\/annurev-arplant-050213-035811","volume":"65","author":"JL Bennetzen","year":"2014","unstructured":"Bennetzen, J. L. & Wang, H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 65, 505\u2013530 (2014).","journal-title":"Annu. Rev. Plant Biol."},{"key":"1955_CR30","doi-asserted-by":"publisher","first-page":"4","DOI":"10.11646\/phytotaxa.652.4.5","volume":"652","author":"Y-W Tang","year":"2024","unstructured":"Tang, Y.-W. et al. Rosa forrestiana var. maculata, a new variety of Rosa (Rosaceae) from Yunnan, China. Phytotaxa 652, 4 (2024).","journal-title":"Phytotaxa"},{"key":"1955_CR31","doi-asserted-by":"publisher","first-page":"61","DOI":"10.3897\/phytokeys.229.101052","volume":"229","author":"L-N Zheng","year":"2023","unstructured":"Zheng, L.-N. et al. Rosa funingensis (Rosaceae), a new species from Yunnan, China. PhytoKeys 229, 61\u201370 (2023).","journal-title":"PhytoKeys"},{"key":"1955_CR32","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1007\/s12225-023-10135-7","volume":"78","author":"P Lyu","year":"2023","unstructured":"Lyu, P. et al. Rosa yangii (Rosaceae), a new species from China. Kew Bull. 78, 663\u2013671 (2023).","journal-title":"Kew Bull."},{"key":"1955_CR33","doi-asserted-by":"publisher","first-page":"169","DOI":"10.11646\/phytotaxa.556.2.6","volume":"556","author":"T Deng","year":"2022","unstructured":"Deng, T. et al. Rosa tomurensis, a new species of Rosa (Rosaceae) from China. Phytotaxa 556, 169\u2013177 (2022).","journal-title":"Phytotaxa"},{"key":"1955_CR34","doi-asserted-by":"publisher","first-page":"4711","DOI":"10.1093\/jxb\/erw269","volume":"67","author":"M Liorzou","year":"2016","unstructured":"Liorzou, M. et al. Nineteenth century French rose Rosa sp. germplasm shows a shift over time from a European to an Asian genetic background. J. Exp. Bot. 67, 4711\u20134725 (2016).","journal-title":"J. Exp. Bot."},{"key":"1955_CR35","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-023-04244-5","volume":"23","author":"F Zang","year":"2023","unstructured":"Zang, F. et al. Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways. BMC Plant Biol. 23, 235 (2023).","journal-title":"BMC Plant Biol."},{"key":"1955_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27054-5","volume":"12","author":"H Ao","year":"2021","unstructured":"Ao, H. et al. Global warming-induced Asian hydrological climate transition across the Miocene\u2013Pliocene boundary. Nat. Commun. 12, 6935 (2021).","journal-title":"Nat. Commun."},{"key":"1955_CR37","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1126\/science.1172873","volume":"325","author":"PU Clark","year":"2009","unstructured":"Clark, P. U. et al. The Last Glacial Maximum. Science 325, 710\u2013714 (2009).","journal-title":"Science"},{"key":"1955_CR38","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1038\/nature435757a","volume":"435","author":"J Ogata","year":"2005","unstructured":"Ogata, J., Kanno, Y., Itoh, Y., Tsugawa, H. & Suzuki, M. Anthocyanin biosynthesis in roses. Nature 435, 757\u2013758 (2005).","journal-title":"Nature"},{"key":"1955_CR39","doi-asserted-by":"publisher","first-page":"239","DOI":"10.5511\/plantbiotechnology.10.1220a","volume":"28","author":"M Fukuchi-Mizutani","year":"2011","unstructured":"Fukuchi-Mizutani, M. et al. Biochemical and molecular characterization of anthocyanidin\/flavonol 3-glucosylation pathways in Rosa\u00d7 hybrida. Plant Biotechnol. 28, 239\u2013244 (2011).","journal-title":"Plant Biotechnol."},{"key":"1955_CR40","doi-asserted-by":"publisher","first-page":"uhad080","DOI":"10.1093\/hr\/uhad080","volume":"10","author":"G He","year":"2023","unstructured":"He, G., Zhang, R., Jiang, S., Wang, H. & Ming, F. The MYB transcription factor RcMYB1 plays a central role in rose anthocyanin biosynthesis. Hortic. Res. 10, uhad080 (2023).","journal-title":"Hortic. Res."},{"key":"1955_CR41","doi-asserted-by":"publisher","first-page":"857684","DOI":"10.3389\/fpls.2022.857684","volume":"13","author":"M Li","year":"2022","unstructured":"Li, M. et al. Rosa1, a transposable element-like insertion, produces red petal coloration in rose through altering RcMYB114 transcription. Front. Plant Sci. 13, 857684 (2022).","journal-title":"Front. Plant Sci."},{"key":"1955_CR42","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1111\/pbi.13123","volume":"17","author":"Y Shen","year":"2019","unstructured":"Shen, Y. et al. RrMYB5- and RrMYB10-regulated flavonoid biosynthesis plays a pivotal role in feedback loop responding to wounding and oxidation in Rosa rugosa. Plant Biotechnol. J. 17, 2078\u20132095 (2019).","journal-title":"Plant Biotechnol. J."},{"key":"1955_CR43","doi-asserted-by":"publisher","first-page":"2325","DOI":"10.1105\/tpc.005207","volume":"14","author":"I Guterman","year":"2002","unstructured":"Guterman, I. et al. Rose scent: genomics approach to discovering novel floral fragrance-related genes. Plant Cell 14, 2325\u20132338 (2002).","journal-title":"Plant Cell"},{"key":"1955_CR44","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1007\/s00122-010-1268-y","volume":"120","author":"M Spiller","year":"2010","unstructured":"Spiller, M., Berger, R. G. & Debener, T. Genetic dissection of scent metabolic profiles in diploid rose populations. Theor. Appl. Genet. 120, 1461\u20131471 (2010).","journal-title":"Theor. Appl. Genet."},{"key":"1955_CR45","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1271\/bbb.70090","volume":"71","author":"M Sakai","year":"2007","unstructured":"Sakai, M. et al. Production of 2-phenylethanol in roses as the dominant floral scent compound from l-phenylalanine by two key enzymes, a PLP-dependent decarboxylase and a phenylacetaldehyde reductase. Biosci. Biotechnol. Biochem. 71, 2408\u20132419 (2007).","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"1955_CR46","doi-asserted-by":"publisher","DOI":"10.1016\/j.hpj.2024.01.002","author":"Y Li","year":"2024","unstructured":"Li, Y. et al. The coordinated interaction or regulation between floral pigments and volatile organic compounds. Hortic. Plant J. https:\/\/doi.org\/10.1016\/j.hpj.2024.01.002 (2024).","journal-title":"Hortic. Plant J."},{"key":"1955_CR47","doi-asserted-by":"publisher","first-page":"1908","DOI":"10.1093\/plphys\/kiae444","volume":"196","author":"H Li","year":"2024","unstructured":"Li, H. et al. The complexity of volatile terpene biosynthesis in roses: particular insights into \u03b2-citronellol production. Plant Physiol. 196, 1908\u20131922 (2024).","journal-title":"Plant Physiol."},{"key":"1955_CR48","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1038\/s41438-021-00512-3","volume":"8","author":"V Soufflet-Freslon","year":"2021","unstructured":"Soufflet-Freslon, V. et al. Diversity and selection of the continuous-flowering gene, RoKSN, in rose. Hortic. Res. 8, 76 (2021).","journal-title":"Hortic. Res."},{"key":"1955_CR49","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1111\/j.1365-313X.2011.04776.x","volume":"69","author":"H Iwata","year":"2012","unstructured":"Iwata, H. et al. The TFL1 homologue KSN is a regulator of continuous flowering in rose and strawberry. Plant J. 69, 116\u2013125 (2012).","journal-title":"Plant J."},{"key":"1955_CR50","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1007\/s00122-005-2042-4","volume":"111","author":"ML Dugo","year":"2005","unstructured":"Dugo, M. L. et al. Genetic mapping of QTLs controlling horticultural traits in diploid roses. Theor. Appl. Genet. 111, 511\u2013520 (2005).","journal-title":"Theor. Appl. Genet."},{"key":"1955_CR51","first-page":"108","volume":"1","author":"L Shubin","year":"2015","unstructured":"Shubin, L. et al. Inheritance of perpetual blooming in Rosa chinensis \u2018Old Blush\u2019. Hortic. Plant J. 1, 108\u2013112 (2015).","journal-title":"Hortic. Plant J."},{"key":"1955_CR52","first-page":"1327","volume":"9","author":"T Kania","year":"1997","unstructured":"Kania, T., Russenberger, D., Peng, S., Apel, K. & Melzer, S. FPF1 promotes flowering in Arabidopsis. Plant Cell 9, 1327\u20131338 (1997).","journal-title":"Plant Cell"},{"key":"1955_CR53","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/s41438-020-00355-4","volume":"7","author":"Y Lei","year":"2020","unstructured":"Lei, Y. et al. Woodland strawberry WRKY71 acts as a promoter of flowering via a transcriptional regulatory cascade. Hortic. Res. 7, 137 (2020).","journal-title":"Hortic. Res."},{"key":"1955_CR54","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/ng1298","volume":"36","author":"H-J Kim","year":"2004","unstructured":"Kim, H.-J. et al. A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana. Nat. Genet. 36, 167\u2013171 (2004).","journal-title":"Nat. Genet."},{"key":"1955_CR55","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s11295-015-0906-6","volume":"11","author":"H Roman","year":"2015","unstructured":"Roman, H. et al. Genetic analysis of the flowering date and number of petals in rose. Tree Genet. Genomes 11, 85 (2015).","journal-title":"Tree Genet. Genomes"},{"key":"1955_CR56","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-30918-4","volume":"8","author":"L Fran\u00e7ois","year":"2018","unstructured":"Fran\u00e7ois, L. et al. A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses. Sci. Rep. 8, 12912 (2018).","journal-title":"Sci. Rep."},{"key":"1955_CR57","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1111\/tpj.14036","volume":"96","author":"S Gattolin","year":"2018","unstructured":"Gattolin, S. et al. Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae. Plant J. 96, 358\u2013371 (2018).","journal-title":"Plant J."},{"key":"1955_CR58","doi-asserted-by":"publisher","first-page":"3299","DOI":"10.1007\/s00122-020-03670-5","volume":"133","author":"DC Lopez Arias","year":"2020","unstructured":"Lopez Arias, D. C. et al. Characterization of black spot resistance in diploid roses with QTL detection, meta-analysis and candidate-gene identification. Theor. Appl. Genet. 133, 3299\u20133321 (2020).","journal-title":"Theor. Appl. Genet."},{"key":"1955_CR59","doi-asserted-by":"publisher","first-page":"111678","DOI":"10.1016\/j.plantsci.2023.111678","volume":"335","author":"XR Li","year":"2023","unstructured":"Li, X. R. et al. Function of two splicing variants of RcCPR5 in the resistance of Rosa chinensis to powdery mildew. Plant Sci. 335, 111678 (2023).","journal-title":"Plant Sci."},{"key":"1955_CR60","doi-asserted-by":"publisher","first-page":"uhad059","DOI":"10.1093\/hr\/uhad059","volume":"10","author":"ZJ Rawandoozi","year":"2023","unstructured":"Rawandoozi, Z. J. et al. QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations. Hortic. Res. 10, uhad059 (2023).","journal-title":"Hortic. Res."},{"key":"1955_CR61","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1186\/1471-2148-8-286","volume":"8","author":"C Radauer","year":"2008","unstructured":"Radauer, C., Lackner, P. & Breiteneder, H. The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. BMC Evol. Biol. 8, 286 (2008).","journal-title":"BMC Evol. Biol."},{"key":"1955_CR62","doi-asserted-by":"publisher","first-page":"uhad238","DOI":"10.1093\/hr\/uhad238","volume":"11","author":"R Li","year":"2024","unstructured":"Li, R. et al. Integrated proteomic analysis reveals interactions between phosphorylation and ubiquitination in rose response to Botrytis infection. Hortic. Res. 11, uhad238 (2024).","journal-title":"Hortic. Res."},{"key":"1955_CR63","unstructured":"Linnaeus, C. Species Plantarum, Holmiae: Impensis Laurentii Salvii, Vol. 1, 491\u2013492 (1753)."},{"key":"1955_CR64","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1093\/sysbio\/syab064","volume":"71","author":"K Debray","year":"2022","unstructured":"Debray, K. et al. Unveiling the patterns of reticulated evolutionary processes with phylogenomics: hybridization and polyploidy in the genus Rosa. Syst. Biol. 71, 547\u2013569 (2022).","journal-title":"Syst. Biol."},{"key":"1955_CR65","doi-asserted-by":"publisher","first-page":"uhab051","DOI":"10.1093\/hr\/uhab051","volume":"9","author":"WH Cui","year":"2022","unstructured":"Cui, W. H. et al. Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China. Hortic. Res. 9, uhab051 (2022).","journal-title":"Hortic. Res."},{"key":"1955_CR66","doi-asserted-by":"crossref","unstructured":"Zhang, C., Li, S.-Q., Xie, H.-H., Liu, J.-Q. & Gao, X.-F. Comparative plastid genome analyses of Rosa: insights into the phylogeny and gene divergence. Tree Genet. Genomes 18, 20 (2022).","DOI":"10.1007\/s11295-022-01549-8"},{"key":"1955_CR67","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1600\/036364407781179653","volume":"32","author":"A Bruneau","year":"2007","unstructured":"Bruneau, A., Starr, J. R. & Joly, S. Phylogenetic relationships in the genus Rosa: new evidence from chloroplast DNA sequences and an appraisal of current knowledge. Syst. Bot. 32, 366\u2013378 (2007).","journal-title":"Syst. Bot."},{"key":"1955_CR68","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.ympev.2015.03.014","volume":"87","author":"Z-M Zhu","year":"2015","unstructured":"Zhu, Z.-M., Gao, X.-F. & Foug\u00e8re-Danezan, M. Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers. Mol. Phylogenet. Evol. 87, 50\u201364 (2015).","journal-title":"Mol. Phylogenet. Evol."},{"key":"1955_CR69","doi-asserted-by":"publisher","first-page":"1618","DOI":"10.21273\/HORTSCI.50.11.1618","volume":"50","author":"CY Liu","year":"2015","unstructured":"Liu, C. Y. et al. Phylogenetic relationships in the genus Rosa revisited based on rpl16, trnL-F, and atpB-rbcL sequences. Hortscience 50, 1618\u20131624 (2015).","journal-title":"Hortscience"},{"key":"1955_CR70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10592-019-01227-8","volume":"21","author":"C Zhang","year":"2020","unstructured":"Zhang, C. et al. Molecular and morphological evidence for hybrid origin and matroclinal inheritance of an endangered wild rose, Rosa\u2009\u00d7\u2009pseudobanksiae (Rosaceae) from China. Conserv. Genet. 21, 1\u201311 (2020).","journal-title":"Conserv. Genet."},{"key":"1955_CR71","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s00606-011-0504-5","volume":"297","author":"J Meng","year":"2011","unstructured":"Meng, J., Foug\u00e8re-Danezan, M., Zhang, L.-B., Li, D.-Z. & Yi, T.-S. Untangling the hybrid origin of the Chinese tea roses: evidence from DNA sequences of single-copy nuclear and chloroplast genes. Plant Syst. Evol. 297, 157\u2013170 (2011).","journal-title":"Plant Syst. Evol."},{"key":"1955_CR72","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1186\/s12862-019-1479-z","volume":"19","author":"K Debray","year":"2019","unstructured":"Debray, K. et al. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol. Biol. 19, 152 (2019).","journal-title":"BMC Evol. Biol."},{"key":"1955_CR73","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1038\/s41586-024-07324-0","volume":"629","author":"AR Zuntini","year":"2024","unstructured":"Zuntini, A. R. et al. Phylogenomics and the rise of the angiosperms. Nature 629, 843\u2013850 (2024).","journal-title":"Nature"},{"key":"1955_CR74","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1093\/jpe\/rtab083","volume":"15","author":"Q Wang","year":"2021","unstructured":"Wang, Q., Guo, Q., Chi, X., Zhu, S. & Tang, Z. Evolutionary history and climate conditions constrain the flower colours of woody plants in China. J. Plant Ecol. 15, 196\u2013207 (2021).","journal-title":"J. Plant Ecol."},{"key":"1955_CR75","doi-asserted-by":"publisher","DOI":"10.1038\/srep11698","volume":"5","author":"Y-D Gao","year":"2015","unstructured":"Gao, Y.-D., Zhang, Y., Gao, X.-F. & Zhu, Z.-M. Pleistocene glaciations, demographic expansion and subsequent isolation promoted morphological heterogeneity: a phylogeographic study of the alpine Rosa sericea complex (Rosaceae). Sci. Rep. 5, 11698 (2015).","journal-title":"Sci. Rep."},{"key":"1955_CR76","doi-asserted-by":"publisher","first-page":"E3444","DOI":"10.1073\/pnas.1616063114","volume":"114","author":"Y Xing","year":"2017","unstructured":"Xing, Y. & Ree, R. H. Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot. Proc. Natl Acad. Sci. USA 114, E3444\u2013E3451 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"1955_CR77","doi-asserted-by":"publisher","first-page":"321","DOI":"10.3389\/fpls.2019.00321","volume":"10","author":"Y-D Gao","year":"2019","unstructured":"Gao, Y.-D., Gao, X.-F. & Harris, A. Species boundaries and parapatric speciation in the complex of alpine shrubs, Rosa sericea (Rosaceae), based on population genetics and ecological tolerances. Front. Plant Sci. 10, 321 (2019).","journal-title":"Front. Plant Sci."},{"key":"1955_CR78","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.palwor.2015.05.010","volume":"25","author":"T Su","year":"2016","unstructured":"Su, T. et al. A Miocene leaf fossil record of Rosa (R. fortuita n. sp.) from its modern diversity center in SW China. Palaeoworld 25, 104\u2013115 (2016).","journal-title":"Palaeoworld"},{"key":"1955_CR79","doi-asserted-by":"publisher","unstructured":"Caissard, J. C., Adrar, I., Conart, C., Paramita, S. N. & Baudino, S. Do we really know the scent of roses? Bot. Lett. https:\/\/doi.org\/10.1080\/23818107.2022.2160807 (2022).","DOI":"10.1080\/23818107.2022.2160807"},{"key":"1955_CR80","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1126\/science.aab0696","volume":"349","author":"JL Magnard","year":"2015","unstructured":"Magnard, J. L. et al. Biosynthesis of monoterpene scent compounds in roses. Science 349, 81\u201383 (2015).","journal-title":"Science"},{"key":"1955_CR81","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1016\/j.tplants.2016.07.007","volume":"21","author":"P Sun","year":"2016","unstructured":"Sun, P., Schuurink, R. C., Caissard, J. C., Hugueney, P. & Baudino, S. My way: noncanonical biosynthesis pathways for plant volatiles. Trends Plant Sci. 21, 884\u2013894 (2016).","journal-title":"Trends Plant Sci."},{"key":"1955_CR82","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1111\/j.1469-8137.2012.04161.x","volume":"195","author":"MM Zvi","year":"2012","unstructured":"Zvi, M. M. et al. PAP1 transcription factor enhances production of phenylpropanoid and terpenoid scent compounds in rose flowers. New Phytol. 195, 335\u2013345 (2012).","journal-title":"New Phytol."},{"key":"1955_CR83","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1016\/j.molp.2015.03.012","volume":"8","author":"JY Liu","year":"2015","unstructured":"Liu, J. Y., Osbourn, A. & Ma, P. D. MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Mol. Plant 8, 689\u2013708 (2015).","journal-title":"Mol. Plant"},{"key":"1955_CR84","doi-asserted-by":"publisher","first-page":"979348","DOI":"10.3389\/fpls.2022.979348","volume":"13","author":"Y Zhai","year":"2022","unstructured":"Zhai, Y. et al. APETALA2\/ethylene responsive factor in fruit ripening: roles, interactions and expression regulation. Front. Plant Sci. 13, 979348 (2022).","journal-title":"Front. Plant Sci."},{"key":"1955_CR85","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1038\/s41438-021-00694-w","volume":"8","author":"QY Dang","year":"2021","unstructured":"Dang, Q. Y. et al. An apple (Malus domestica) AP2\/ERF transcription factor modulates carotenoid accumulation. Hortic. Res. 8, 223 (2021).","journal-title":"Hortic. Res."},{"key":"1955_CR86","doi-asserted-by":"publisher","first-page":"4105","DOI":"10.1093\/jxb\/erw189","volume":"67","author":"SL Shen","year":"2016","unstructured":"Shen, S. L. et al. CitAP2.10 activation of the terpene synthase CsTPS1 is associated with the synthesis of (+)-valencene in \u2018Newhall\u2019 orange. J. Exp. Bot. 67, 4105\u20134115 (2016).","journal-title":"J. Exp. Bot."},{"key":"1955_CR87","doi-asserted-by":"publisher","first-page":"111200","DOI":"10.1016\/j.plantsci.2022.111200","volume":"317","author":"CY Wei","year":"2022","unstructured":"Wei, C. Y. et al. Linalool synthesis related PpTPS1 and PpTPS3 are activated by transcription factor PpERF61 whose expression is associated with DNA methylation during peach fruit ripening. Plant Sci. 317, 111200 (2022).","journal-title":"Plant Sci."},{"key":"1955_CR88","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1111\/tpj.12712","volume":"80","author":"LG Cui","year":"2014","unstructured":"Cui, L. G., Shan, J. X., Shi, M., Gao, J. P. & Lin, H. X. The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J. 80, 1108\u20131117 (2014).","journal-title":"Plant J."},{"key":"1955_CR89","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.molp.2014.11.002","volume":"8","author":"Z-X Yu","year":"2015","unstructured":"Yu, Z.-X. et al. Progressive regulation of sesquiterpene biosynthesis in Arabidopsis and patchouli (Pogostemon cablin) by the miR156-targeted SPL transcription factors. Mol. Plant 8, 98\u2013110 (2015).","journal-title":"Mol. Plant"},{"key":"1955_CR90","doi-asserted-by":"publisher","first-page":"113402","DOI":"10.1016\/j.scienta.2024.113402","volume":"336","author":"ZQ Zhu","year":"2024","unstructured":"Zhu, Z. Q. et al. An O-methyltransferase gene, RrCCoAOMT1, participates in the red flower color formation of Rosa rugosa. Sci. Hortic. 336, 113402 (2024).","journal-title":"Sci. Hortic."},{"key":"1955_CR91","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28732-8","volume":"13","author":"H Yu","year":"2022","unstructured":"Yu, H. & Li, J. Y. Breeding future crops to feed the world through de novo domestication. Nat. Commun. 13, 1171 (2022).","journal-title":"Nat. Commun."},{"key":"1955_CR92","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1038\/nbt.4272","volume":"36","author":"A Zs\u00f6g\u00f6n","year":"2018","unstructured":"Zs\u00f6g\u00f6n, A. et al. De novo domestication of wild tomato using genome editing. Nat. Biotechnol. 36, 1211\u20131216 (2018).","journal-title":"Nat. Biotechnol."},{"key":"1955_CR93","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02134-9","volume":"21","author":"A Rhie","year":"2020","unstructured":"Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).","journal-title":"Genome Biol."},{"key":"1955_CR94","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Simao","year":"2015","unstructured":"Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210\u20133212 (2015).","journal-title":"Bioinformatics"},{"key":"1955_CR95","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows\u2013Wheeler transform. Bioinformatics 26, 589\u2013595 (2010).","journal-title":"Bioinformatics"},{"key":"1955_CR96","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"1955_CR97","doi-asserted-by":"publisher","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","volume":"13","author":"CJ Chen","year":"2020","unstructured":"Chen, C. J. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data.Mol. Plant 13, 1194\u20131202 (2020).","journal-title":"Mol. Plant"},{"key":"1955_CR98","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"LT Nguyen","year":"2015","unstructured":"Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268\u2013274 (2015).","journal-title":"Mol. Biol. Evol."},{"key":"1955_CR99","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02154-5","volume":"21","author":"JJ Jin","year":"2020","unstructured":"Jin, J. J. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21, 241 (2020).","journal-title":"Genome Biol."},{"key":"1955_CR100","doi-asserted-by":"publisher","DOI":"10.1186\/s13007-019-0435-7","volume":"15","author":"XJ Qu","year":"2019","unstructured":"Qu, X. J., Moore, M. J., Li, D. Z. & Yi, T. S. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods 15, 50 (2019).","journal-title":"Plant Methods"},{"key":"1955_CR101","doi-asserted-by":"publisher","first-page":"3718","DOI":"10.1093\/bioinformatics\/btv428","volume":"31","author":"T Galili","year":"2015","unstructured":"Galili, T. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31, 3718\u20133720 (2015).","journal-title":"Bioinformatics"},{"key":"1955_CR102","unstructured":"Maddison, W. P. and Maddison, D. R. Mesquite: a modular system for evolutionary analysis. Version 3.81. (2023); http:\/\/www.mesquiteproject.org ."},{"key":"1955_CR103","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655\u20131664 (2009).","journal-title":"Genome Res."},{"key":"1955_CR104","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559\u2013575 (2007).","journal-title":"Am. J. Hum. Genet."},{"key":"1955_CR105","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1093\/bioinformatics\/bty875","volume":"35","author":"C Zhang","year":"2018","unstructured":"Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M. & Yang, T.-L. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786\u20131788 (2018).","journal-title":"Bioinformatics"},{"key":"1955_CR106","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1186\/s12859-023-05318-9","volume":"24","author":"RL Zhang","year":"2023","unstructured":"Zhang, R. L., Jia, G. Q. & Diao, X. M. geneHapR: an R package for gene haplotypic statistics and visualization. BMC Bioinformatics 24, 199 (2023).","journal-title":"BMC Bioinformatics"},{"key":"1955_CR107","doi-asserted-by":"crossref","unstructured":"Rosyara, U. R., De Jong, W. S., Douches, D. S. & Endelman, J. B. Software for genome-wide association studies in autopolyploids and its application to potato. Plant Genome 9, plantgenome2015.08.0073 (2016).","DOI":"10.3835\/plantgenome2015.08.0073"},{"key":"1955_CR108","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156\u20132158 (2011).","journal-title":"Bioinformatics"},{"key":"1955_CR109","doi-asserted-by":"publisher","first-page":"e1002967","DOI":"10.1371\/journal.pgen.1002967","volume":"8","author":"JK Pickrell","year":"2012","unstructured":"Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012).","journal-title":"PLoS Genet."},{"key":"1955_CR110","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1111\/1755-0998.13265","volume":"21","author":"M Malinsky","year":"2021","unstructured":"Malinsky, M., Matschiner, M. & Svardal, H. Dsuite - fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584\u2013595 (2021).","journal-title":"Mol. Ecol. Resour."},{"key":"1955_CR111","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02196-9","volume":"21","author":"X Liu","year":"2020","unstructured":"Liu, X. & Fu, Y. X. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280 (2020).","journal-title":"Genome Biol."},{"key":"1955_CR112","first-page":"555","volume":"13","author":"Z Yang","year":"1997","unstructured":"Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555\u2013556 (1997).","journal-title":"Comput. Appl. Biosci."}],"container-title":["Nature Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41477-025-01955-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41477-025-01955-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41477-025-01955-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T08:04:48Z","timestamp":1745395488000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41477-025-01955-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,4]]},"references-count":112,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["1955"],"URL":"https:\/\/doi.org\/10.1038\/s41477-025-01955-5","relation":{},"ISSN":["2055-0278"],"issn-type":[{"value":"2055-0278","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,4]]},"assertion":[{"value":"15 December 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 February 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 April 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}