{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T09:41:47Z","timestamp":1792748507945,"version":"4.5.0"},"reference-count":152,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["SYS202206, ZR2023JQ010"],"award-info":[{"award-number":["SYS202206, ZR2023JQ010"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012620","name":"Taishan Scholar Foundation of Shandong Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012620","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat. Plants"],"DOI":"10.1038\/s41477-026-02442-1","type":"journal-article","created":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T09:01:44Z","timestamp":1792746104000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-level phylogenomics and genome evolution of the grape family"],"prefix":"10.1038","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-2883-8282","authenticated-orcid":false,"given":"Xiangfeng","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6139-9588","authenticated-orcid":false,"given":"Jingxuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuenan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoying","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyun","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9642-5268","authenticated-orcid":false,"given":"Xinhe","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Falak Sher","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Mei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linling","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haisheng","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chonghuai","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5091-9133","authenticated-orcid":false,"given":"Naomi","family":"Abe-Kanoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3464-507X","authenticated-orcid":false,"given":"Wenxiu","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6100-3481","authenticated-orcid":false,"given":"Li","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,23]]},"reference":[{"key":"2442_CR1","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1111\/jse.12427","volume":"56","author":"J Wen","year":"2018","unstructured":"Wen, J. et al. A new phylogenetic tribal classification of the grape family (Vitaceae). J. Syst. Evol. 56, 262\u2013272 (2018).","journal-title":"J. Syst. Evol."},{"key":"2442_CR2","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1126\/science.add8655","volume":"379","author":"Y Dong","year":"2023","unstructured":"Dong, Y. et al. Dual domestications and origin of traits in grapevine evolution. Science 379, 892\u2013901 (2023).","journal-title":"Science"},{"key":"2442_CR3","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1038\/s41477-024-01726-8","volume":"10","author":"Y You","year":"2024","unstructured":"You, Y. et al. Transition of survival strategies under global climate shifts in the grape family. Nat. Plants 10, 1100\u20131111 (2024).","journal-title":"Nat. Plants"},{"key":"2442_CR4","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2020.106948","volume":"154","author":"ZY Ma","year":"2021","unstructured":"Ma, Z. Y. et al. Phylogenomic relationships and character evolution of the grape family (Vitaceae). Mol. Phylogenet. Evol. 154, 106948 (2021).","journal-title":"Mol. Phylogenet. Evol."},{"key":"2442_CR5","doi-asserted-by":"publisher","first-page":"e74394","DOI":"10.1371\/journal.pone.0074394","volume":"8","author":"J Wen","year":"2013","unstructured":"Wen, J. et al. Transcriptome sequences resolve deep relationships of the grape family. PLOS ONE 8, e74394 (2013).","journal-title":"PLOS ONE"},{"key":"2442_CR6","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1111\/cla.12191","volume":"34","author":"L Lu","year":"2018","unstructured":"Lu, L. et al. Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae). Cladistics 34, 57\u201377 (2018).","journal-title":"Cladistics"},{"key":"2442_CR7","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":"2442_CR8","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/s41588-025-02111-7","volume":"57","author":"L Guo","year":"2025","unstructured":"Guo, L. et al. Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement. Nat. Genet. 57, 741\u2013753 (2025).","journal-title":"Nat. Genet."},{"key":"2442_CR9","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-03133-2","volume":"24","author":"N Cochetel","year":"2023","unstructured":"Cochetel, N. et al. A super-pangenome of the North American wild grape species. Genome Biol. 24, 290 (2023).","journal-title":"Genome Biol."},{"key":"2442_CR10","doi-asserted-by":"publisher","first-page":"2804","DOI":"10.1038\/s41588-024-01967-5","volume":"56","author":"Z Liu","year":"2024","unstructured":"Liu, Z. et al. Grapevine pangenome facilitates trait genetics and genomic breeding. Nat. Genet. 56, 2804\u20132814 (2024).","journal-title":"Nat. Genet."},{"key":"2442_CR11","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1038\/s41477-019-0507-8","volume":"5","author":"Y Zhou","year":"2019","unstructured":"Zhou, Y. et al. The population genetics of structural variants in grapevine domestication. Nat. Plants 5, 965\u2013979 (2019).","journal-title":"Nat. Plants"},{"key":"2442_CR12","doi-asserted-by":"publisher","first-page":"dsac040","DOI":"10.1093\/dnares\/dsac040","volume":"29","author":"K Shirasawa","year":"2022","unstructured":"Shirasawa, K. et al. De novo whole-genome assembly in an interspecific hybrid table grape, \u2018Shine Muscat\u2019. DNA Res. 29, dsac040 (2022).","journal-title":"DNA Res."},{"key":"2442_CR13","doi-asserted-by":"publisher","first-page":"uhad061","DOI":"10.1093\/hr\/uhad061","volume":"10","author":"X Shi","year":"2023","unstructured":"Shi, X. et al. The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic. Res. 10, uhad061 (2023).","journal-title":"Hortic. Res."},{"key":"2442_CR14","doi-asserted-by":"publisher","first-page":"uhad260","DOI":"10.1093\/hr\/uhad260","volume":"11","author":"X Wang","year":"2024","unstructured":"Wang, X. et al. Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics. Hortic. Res. 11, uhad260 (2024).","journal-title":"Hortic. Res."},{"key":"2442_CR15","doi-asserted-by":"publisher","first-page":"1879","DOI":"10.1111\/nph.20376","volume":"245","author":"S Steckenborn","year":"2025","unstructured":"Steckenborn, S. & Marques, A. Centromere diversity and its evolutionary impacts on plant karyotypes and plant reproduction. New Phytol. 245, 1879\u20131886 (2025).","journal-title":"New Phytol."},{"key":"2442_CR16","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/S0169-5347(01)02187-5","volume":"16","author":"LH Rieseberg","year":"2001","unstructured":"Rieseberg, L. H. Chromosomal rearrangements and speciation. Trends Ecol. Evol. 16, 351\u2013358 (2001).","journal-title":"Trends Ecol. Evol."},{"key":"2442_CR17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2313921121","volume":"121","author":"P Sun","year":"2024","unstructured":"Sun, P. et al. Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family. Proc. Natl Acad. Sci. USA 121, e2313921121 (2024).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2442_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-59640-2","volume":"16","author":"X Jiang","year":"2025","unstructured":"Jiang, X. et al. Chromosome fusions shaped karyotype evolution and evolutionary relationships in the model family Brassicaceae. Nat. Commun. 16, 4631 (2025).","journal-title":"Nat. Commun."},{"key":"2442_CR19","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/nature06148","volume":"449","author":"O Jaillon","year":"2007","unstructured":"Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463\u2013467 (2007).","journal-title":"Nature"},{"key":"2442_CR20","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1093\/gbe\/evv014","volume":"7","author":"F Murat","year":"2015","unstructured":"Murat, F. et al. Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biol. Evol. 7, 735\u2013749 (2015).","journal-title":"Genome Biol. Evol."},{"key":"2442_CR21","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1016\/j.molp.2022.10.018","volume":"15","author":"P Sun","year":"2022","unstructured":"Sun, P. et al. WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol. Plant 15, 1841\u20131851 (2022).","journal-title":"Mol. Plant"},{"key":"2442_CR22","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1007\/s13237-010-0009-6","volume":"53","author":"SP Karkamkar","year":"2010","unstructured":"Karkamkar, S. P., Patil, S. G. & Misra, S. C. Cyto\u2013morphological studies and their significance in evolution of family Vitaceae. Nucleus 53, 37\u201343 (2010).","journal-title":"Nucleus"},{"key":"2442_CR23","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1111\/tpj.16169","volume":"114","author":"S Zhu","year":"2023","unstructured":"Zhu, S. et al. Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids. Plant J. 114, 805\u2013823 (2023).","journal-title":"Plant J."},{"key":"2442_CR24","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhac208","volume":"9","author":"H Xin","year":"2022","unstructured":"Xin, H. et al. A genome for Cissus illustrates features underlying its evolutionary success in dry savannas. Hortic. Res. 9, uhac208 (2022).","journal-title":"Hortic. Res."},{"key":"2442_CR25","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhae038","volume":"11","author":"Q Li","year":"2024","unstructured":"Li, Q. et al. The Cissus quadrangularis genome reveals its adaptive features in an arid habitat. Hortic. Res. 11, uhae038 (2024).","journal-title":"Hortic. Res."},{"key":"2442_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-61387-9","volume":"16","author":"M Massonnet","year":"2025","unstructured":"Massonnet, M. et al. Evolutionary conservation of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae. Nat. Commun. 16, 6047 (2025).","journal-title":"Nat. Commun."},{"key":"2442_CR27","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/s41588-024-02059-0","volume":"57","author":"S Xia","year":"2025","unstructured":"Xia, S., Chen, J., Arsala, D., Emerson, J. J. & Long, M. Functional innovation through new genes as a general evolutionary process. Nat. Genet. 57, 295\u2013309 (2025).","journal-title":"Nat. Genet."},{"key":"2442_CR28","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1038\/271501a0","volume":"271","author":"W Gilbert","year":"1978","unstructured":"Gilbert, W. Why genes in pieces? Nature 271, 501 (1978).","journal-title":"Nature"},{"key":"2442_CR29","doi-asserted-by":"publisher","DOI":"10.1126\/science.1246338","volume":"346","author":"Q Zhou","year":"2014","unstructured":"Zhou, Q. et al. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science 346, 1246338 (2014).","journal-title":"Science"},{"key":"2442_CR30","doi-asserted-by":"publisher","DOI":"10.1038\/nplants.2016.167","volume":"2","author":"X Gan","year":"2016","unstructured":"Gan, X. et al. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nat. Plants 2, 16167 (2016).","journal-title":"Nat. Plants"},{"key":"2442_CR31","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1093\/plphys\/kiae039","volume":"195","author":"Q Long","year":"2024","unstructured":"Long, Q. et al. Population comparative genomics discovers gene gain and loss during grapevine domestication. Plant Physiol. 195, 1401\u20131413 (2024).","journal-title":"Plant Physiol."},{"key":"2442_CR32","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1111\/nph.19861","volume":"243","author":"M Paineau","year":"2024","unstructured":"Paineau, M. et al. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew. New Phytol. 243, 1490\u20131505 (2024).","journal-title":"New Phytol."},{"key":"2442_CR33","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1038\/s41477-024-01901-x","volume":"11","author":"SX Li","year":"2025","unstructured":"Li, S. X., Liu, Y., Zhang, Y. M., Chen, J. Q. & Shao, Z. Q. Convergent reduction of immune receptor repertoires during plant adaptation to diverse special lifestyles and habitats. Nat. Plants 11, 248\u2013262 (2025).","journal-title":"Nat. Plants"},{"key":"2442_CR34","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1016\/j.molp.2021.08.001","volume":"14","author":"Y Liu","year":"2021","unstructured":"Liu, Y. et al. An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion. Mol. Plant 14, 2015\u20132031 (2021).","journal-title":"Mol. Plant"},{"key":"2442_CR35","doi-asserted-by":"publisher","first-page":"2491","DOI":"10.1093\/plcell\/koae113","volume":"36","author":"KS Chia","year":"2024","unstructured":"Chia, K. S. et al. The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages. Plant Cell 36, 2491\u20132511 (2024).","journal-title":"Plant Cell"},{"key":"2442_CR36","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.1111\/tpj.16919","volume":"119","author":"XY Feng","year":"2024","unstructured":"Feng, X. Y., Li, Q., Liu, Y., Zhang, Y. M. & Shao, Z. Q. Evolutionary and immune-activating character analyses of NLR genes in algae suggest the ancient origin of plant intracellular immune receptors. Plant J. 119, 2316\u20132330 (2024).","journal-title":"Plant J."},{"key":"2442_CR37","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1093\/plcell\/koaa002","volume":"33","author":"AC Barragan","year":"2021","unstructured":"Barragan, A. C. & Weigel, D. Plant NLR diversity: the known unknowns of pan-NLRomes. Plant Cell 33, 814\u2013831 (2021).","journal-title":"Plant Cell"},{"key":"2442_CR38","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/s41586-022-04822-x","volume":"606","author":"D Tang","year":"2022","unstructured":"Tang, D. et al. Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535\u2013541 (2022).","journal-title":"Nature"},{"key":"2442_CR39","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1016\/j.cell.2019.07.038","volume":"178","author":"AL Van de Weyer","year":"2019","unstructured":"Van de Weyer, A. L. et al. A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana. Cell 178, 1260\u20131272 (2019).","journal-title":"Cell"},{"key":"2442_CR40","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1038\/s41422-022-00685-z","volume":"32","author":"L Shang","year":"2022","unstructured":"Shang, L. et al. A super pan-genomic landscape of rice. Cell Res. 32, 878\u2013896 (2022).","journal-title":"Cell Res."},{"key":"2442_CR41","doi-asserted-by":"publisher","first-page":"2249","DOI":"10.1111\/tpj.16705","volume":"118","author":"C Mo","year":"2024","unstructured":"Mo, C. et al. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. Plant J. 118, 2249\u20132268 (2024).","journal-title":"Plant J."},{"key":"2442_CR42","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1038\/s41586-024-08277-0","volume":"637","author":"C Jiao","year":"2025","unstructured":"Jiao, C. et al. Pan-genome bridges wheat structural variations with habitat and breeding. Nature 637, 384\u2013393 (2025).","journal-title":"Nature"},{"key":"2442_CR43","doi-asserted-by":"publisher","first-page":"1579","DOI":"10.1038\/s41588-023-01486-9","volume":"55","author":"X Lin","year":"2023","unstructured":"Lin, X. et al. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat. Genet. 55, 1579\u20131588 (2023).","journal-title":"Nat. Genet."},{"key":"2442_CR44","doi-asserted-by":"publisher","first-page":"8714","DOI":"10.1073\/pnas.151269298","volume":"98","author":"VV Kapitonov","year":"2001","unstructured":"Kapitonov, V. V. & Jurka, J. Rolling-circle transposons in eukaryotes. Proc. Natl Acad. Sci. USA 98, 8714\u20138719 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2442_CR45","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms10716","volume":"7","author":"I Grabundzija","year":"2016","unstructured":"Grabundzija, I. et al. A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes. Nat. Commun. 7, 10716 (2016).","journal-title":"Nat. Commun."},{"key":"2442_CR46","doi-asserted-by":"publisher","unstructured":"Thomas, J. & Pritham, E. J. Helitrons, the eukaryotic rolling-circle transposable elements. Microbiol. Spectr. 3, https:\/\/doi.org\/10.1128\/microbiolspec.mdna3-0049-2014 (2015).","DOI":"10.1128\/microbiolspec.mdna3-0049-2014"},{"key":"2442_CR47","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.plantsci.2008.11.004","volume":"176","author":"S Lal","year":"2009","unstructured":"Lal, S., Oetjens, M. & Hannah, L. C. Helitrons: enigmatic abductors and mobilizers of host genome sequences. Plant Sci. 176, 181\u2013186 (2009).","journal-title":"Plant Sci."},{"key":"2442_CR48","doi-asserted-by":"publisher","first-page":"19916","DOI":"10.1073\/pnas.0904742106","volume":"106","author":"C Du","year":"2009","unstructured":"Du, C., Fefelova, N., Caronna, J., He, L. & Dooner, H. K. The polychromatic Helitron landscape of the maize genome. Proc. Natl Acad. Sci. USA 106, 19916\u201319921 (2009).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2442_CR49","doi-asserted-by":"publisher","first-page":"1052","DOI":"10.1111\/tpj.14489","volume":"100","author":"SN Anderson","year":"2019","unstructured":"Anderson, S. N. et al. Transposable elements contribute to dynamic genome content in maize. Plant J. 100, 1052\u20131065 (2019).","journal-title":"Plant J."},{"key":"2442_CR50","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-12-609","volume":"12","author":"Y Dong","year":"2011","unstructured":"Dong, Y. et al. Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome. BMC Genomics 12, 609 (2011).","journal-title":"BMC Genomics"},{"key":"2442_CR51","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1126\/science.1178534","volume":"326","author":"PS Schnable","year":"2009","unstructured":"Schnable, P. S. et al. The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112\u20131115 (2009).","journal-title":"Science"},{"key":"2442_CR52","doi-asserted-by":"publisher","first-page":"117793222413089","DOI":"10.1177\/11779322241308944","volume":"19","author":"M Smith","year":"2025","unstructured":"Smith, M., Jones, J. T. & Hein, I. Resistify: a novel NLR classifier that reveals Helitron-associated NLR expansion in solanaceae. Bioinform. Biol. Insights 19, 11779322241308944 (2025).","journal-title":"Bioinform. Biol. Insights"},{"key":"2442_CR53","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1038\/s41592-024-02269-8","volume":"21","author":"H Cheng","year":"2024","unstructured":"Cheng, H., Asri, M., Lucas, J., Koren, S. & Li, H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat. Methods 21, 967\u2013970 (2024).","journal-title":"Nat. Methods"},{"key":"2442_CR54","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","volume":"36","author":"D Guan","year":"2020","unstructured":"Guan, D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36, 2896\u20132898 (2020).","journal-title":"Bioinformatics"},{"key":"2442_CR55","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95\u201398 (2016).","journal-title":"Cell Syst."},{"key":"2442_CR56","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92\u201395 (2017).","journal-title":"Science"},{"key":"2442_CR57","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99\u2013101 (2016).","journal-title":"Cell Syst."},{"key":"2442_CR58","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni, M., Berkeley, M. R., Seppey, M., Sim\u00e3o, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647\u20134654 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"2442_CR59","doi-asserted-by":"publisher","first-page":"1","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, 1\u201327 (2020).","journal-title":"Genome Biol."},{"key":"2442_CR60","volume":"46","author":"S Ou","year":"2018","unstructured":"Ou, S., Chen, J. & Jiang, N. Assessing genome assembly quality using the LTR assembly index (LAI). Nucleic Acids Res. 46, e126 (2018).","journal-title":"Nucleic Acids Res."},{"key":"2442_CR61","doi-asserted-by":"publisher","first-page":"1372","DOI":"10.1111\/tpj.16675","volume":"118","author":"WQ Xu","year":"2024","unstructured":"Xu, W. Q. et al. Genome sequences and population genomics reveal climatic adaptation and genomic divergence between two closely related sweetgum species. Plant J. 118, 1372\u20131387 (2024).","journal-title":"Plant J."},{"key":"2442_CR62","doi-asserted-by":"publisher","first-page":"msac174","DOI":"10.1093\/molbev\/msac174","volume":"39","author":"S Kumar","year":"2022","unstructured":"Kumar, S. et al. TimeTree 5: an expanded resource for species divergence times. Mol. Biol. Evol. 39, msac174 (2022).","journal-title":"Mol. Biol. Evol."},{"key":"2442_CR63","doi-asserted-by":"publisher","first-page":"5516","DOI":"10.1093\/bioinformatics\/btaa1022","volume":"36","author":"FK Mendes","year":"2021","unstructured":"Mendes, F. K., Vanderpool, D., Fulton, B. & Hahn, M. W. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36, 5516\u20135518 (2021).","journal-title":"Bioinformatics"},{"key":"2442_CR64","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2129-y","volume":"19","author":"C Zhang","year":"2018","unstructured":"Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19, 153 (2018).","journal-title":"BMC Bioinformatics"},{"key":"2442_CR65","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/s41586-024-07447-4","volume":"629","author":"JN Wan","year":"2024","unstructured":"Wan, J. N. et al. The rise of baobab trees in Madagascar. Nature 629, 1091\u20131099 (2024).","journal-title":"Nature"},{"key":"2442_CR66","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1126\/science.aaw2090","volume":"366","author":"NB Edelman","year":"2019","unstructured":"Edelman, N. B. et al. Genomic architecture and introgression shape a butterfly radiation. Science 366, 594\u2013599 (2019).","journal-title":"Science"},{"key":"2442_CR67","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1038\/s41477-025-01905-1","volume":"11","author":"K Zhang","year":"2025","unstructured":"Zhang, K. et al. Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers. Nat. Plants 11, 359\u2013375 (2025).","journal-title":"Nat. Plants"},{"key":"2442_CR68","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1111\/pbi.14570","volume":"23","author":"Y Huang","year":"2025","unstructured":"Huang, Y., Sahu, S. K. & Liu, X. Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies. Plant Biotechnol. J. 23, 1121\u20131132 (2025).","journal-title":"Plant Biotechnol. J."},{"key":"2442_CR69","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1038\/s41588-024-01823-6","volume":"56","author":"Y Zhang","year":"2024","unstructured":"Zhang, Y. et al. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat. Genet. 56, 1750\u20131761 (2024).","journal-title":"Nat. Genet."},{"key":"2442_CR70","doi-asserted-by":"publisher","first-page":"9451","DOI":"10.1073\/pnas.1921046117","volume":"117","author":"JM Flynn","year":"2020","unstructured":"Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451\u20139457 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2442_CR71","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1089\/152791600319259","volume":"1","author":"D Nishimura","year":"2000","unstructured":"Nishimura, D. RepeatMasker. Biotech Softw. Internet Rep. 1, 36\u201339 (2000).","journal-title":"Biotech Softw. Internet Rep."},{"key":"2442_CR72","doi-asserted-by":"publisher","first-page":"uhac017","DOI":"10.1093\/hr\/uhac017","volume":"9","author":"RG Zhang","year":"2022","unstructured":"Zhang, R. G. et al. TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes. Hortic. Res. 9, uhac017 (2022).","journal-title":"Hortic. Res."},{"key":"2442_CR73","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09135-8","volume":"10","author":"Z Liang","year":"2019","unstructured":"Liang, Z. et al. Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses. Nat. Commun. 10, 1190 (2019).","journal-title":"Nat. Commun."},{"key":"2442_CR74","doi-asserted-by":"publisher","first-page":"19945","DOI":"10.1073\/pnas.1014330107","volume":"107","author":"RJ Britten","year":"2010","unstructured":"Britten, R. J. Transposable element insertions have strongly affected human evolution. Proc. Natl Acad. Sci. USA 107, 19945\u201319948 (2010).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2442_CR75","doi-asserted-by":"publisher","first-page":"98","DOI":"10.5808\/GI.2014.12.3.98","volume":"12","author":"S Ayarpadikannan","year":"2014","unstructured":"Ayarpadikannan, S. & Kim, H. S. The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genomics Inform. 12, 98\u2013104 (2014).","journal-title":"Genomics Inform."},{"key":"2442_CR76","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.1016\/j.molp.2021.06.017","volume":"14","author":"K Li","year":"2021","unstructured":"Li, K. et al. Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution. Mol. Plant 14, 1745\u20131756 (2021).","journal-title":"Mol. Plant"},{"key":"2442_CR77","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/s41580-022-00457-y","volume":"23","author":"R Fueyo","year":"2022","unstructured":"Fueyo, R., Judd, J., Feschotte, C. & Wysocka, J. Roles of transposable elements in the regulation of mammalian transcription. Nat. Rev. Mol. Cell Biol. 23, 481\u2013497 (2022).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2442_CR78","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1038\/s41586-024-08476-9","volume":"640","author":"L Cheng","year":"2025","unstructured":"Cheng, L. et al. Leveraging a phased pangenome for haplotype design of hybrid potato. Nature 640, 408\u2013417 (2025).","journal-title":"Nature"},{"key":"2442_CR79","doi-asserted-by":"publisher","first-page":"1676","DOI":"10.1016\/j.molp.2020.10.002","volume":"13","author":"W Ouyang","year":"2020","unstructured":"Ouyang, W., Xiong, D., Li, G. & Li, X. Unraveling the 3D genome architecture in plants: present and future. Mol. Plant 13, 1676\u20131693 (2020).","journal-title":"Mol. Plant"},{"key":"2442_CR80","doi-asserted-by":"publisher","first-page":"4729","DOI":"10.1016\/j.molcel.2024.10.031","volume":"84","author":"J Shu","year":"2024","unstructured":"Shu, J. et al. EMF1 functions as a 3D chromatin modulator in Arabidopsis. Mol. Cell 84, 4729\u20134739 (2024).","journal-title":"Mol. Cell"},{"key":"2442_CR81","doi-asserted-by":"publisher","first-page":"1959","DOI":"10.1038\/s41588-022-01237-2","volume":"54","author":"M Wang","year":"2022","unstructured":"Wang, M. et al. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat. Genet. 54, 1959\u20131971 (2022).","journal-title":"Nat. Genet."},{"key":"2442_CR82","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02854-8","volume":"24","author":"L Ni","year":"2023","unstructured":"Ni, L. et al. Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes. Genome Biol. 24, 12 (2023).","journal-title":"Genome Biol."},{"key":"2442_CR83","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1038\/nature14450","volume":"523","author":"E Crane","year":"2015","unstructured":"Crane, E. et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 523, 240\u2013244 (2015).","journal-title":"Nature"},{"key":"2442_CR84","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1104\/pp.19.01273","volume":"183","author":"B Steuernagel","year":"2020","unstructured":"Steuernagel, B. et al. The NLR-annotator tool enables annotation of the intracellular immune receptor repertoire. Plant Physiol. 183, 468\u2013482 (2020).","journal-title":"Plant Physiol."},{"key":"2442_CR85","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/s41588-018-0040-0","volume":"50","author":"JC Stein","year":"2018","unstructured":"Stein, J. C. et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat. Genet. 50, 285\u2013296 (2018).","journal-title":"Nat. Genet."},{"key":"2442_CR86","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1126\/science.338.6108.758","volume":"338","author":"NV Fedoroff","year":"2012","unstructured":"Fedoroff, N. V. Transposable elements, epigenetics, and genome evolution. Science 338, 758\u2013767 (2012).","journal-title":"Science"},{"key":"2442_CR87","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/j.tig.2024.02.002","volume":"40","author":"D Barro-Trastoy","year":"2024","unstructured":"Barro-Trastoy, D. & K\u00f6hler, C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet. 40, 437\u2013448 (2024).","journal-title":"Trends Genet."},{"key":"2442_CR88","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1105\/tpc.008375","volume":"15","author":"SK Lal","year":"2003","unstructured":"Lal, S. K., Giroux, M. J., Brendel, V., Vallejos, C. E. & Hannah, L. C. The maize genome contains a Helitron insertion. Plant Cell 15, 381\u2013391 (2003).","journal-title":"Plant Cell"},{"key":"2442_CR89","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1038\/s41477-024-01717-9","volume":"10","author":"F Herrera","year":"2024","unstructured":"Herrera, F., Carvalho, M. R., Stull, G. W., Jaramillo, C. & Manchester, S. R. Cenozoic seeds of Vitaceae reveal a deep history of extinction and dispersal in the Neotropics. Nat. Plants 10, 1091\u20131099 (2024).","journal-title":"Nat. Plants"},{"key":"2442_CR90","doi-asserted-by":"publisher","first-page":"e0144701","DOI":"10.1371\/journal.pone.0144701","volume":"10","author":"N Zhang","year":"2015","unstructured":"Zhang, N., Wen, J. & Zimmer, E. A. Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming. PLOS ONE 10, e0144701 (2015).","journal-title":"PLOS ONE"},{"key":"2442_CR91","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1002\/tax.603001","volume":"60","author":"H Ren","year":"2011","unstructured":"Ren, H. et al. Phylogenetic analysis of the grape family (Vitaceae) based on the noncoding plastid trnC-petN, trnH-psbA, and trnL-F sequences. Taxon 60, 629\u2013637 (2011).","journal-title":"Taxon"},{"key":"2442_CR92","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1600\/036364412X656437","volume":"37","author":"A Trias-Blasi","year":"2012","unstructured":"Trias-Blasi, A., Parnell, J. A. N. & Hodkinson, T. R. Multi-gene region phylogenetic analysis of the grape family (Vitaceae). Syst. Bot. 37, 941\u2013950 (2012).","journal-title":"Syst. Bot."},{"key":"2442_CR93","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1086\/657283","volume":"172","author":"I Chen","year":"2011","unstructured":"Chen, I. & Manchester, S. R. Seed morphology of Vitaceae. Int. J. Plant Sci. 172, 1\u201335 (2011).","journal-title":"Int. J. Plant Sci."},{"key":"2442_CR94","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1111\/tpj.15381","volume":"107","author":"Q Zhao","year":"2021","unstructured":"Zhao, Q. et al. Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis. Plant J. 107, 1243\u20131259 (2021).","journal-title":"Plant J."},{"key":"2442_CR95","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20442","volume":"17","author":"M Laforest","year":"2024","unstructured":"Laforest, M. et al. The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: insights from the genomes of common and giant ragweed. Plant Genome 17, e20442 (2024).","journal-title":"Plant Genome"},{"key":"2442_CR96","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.100878","volume":"5","author":"J Liu","year":"2024","unstructured":"Liu, J. et al. Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. Plant Commun. 5, 100878 (2024).","journal-title":"Plant Commun."},{"key":"2442_CR97","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43270-7","volume":"14","author":"T Wang","year":"2023","unstructured":"Wang, T. et al. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat. Commun. 14, 7377 (2023).","journal-title":"Nat. Commun."},{"key":"2442_CR98","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-023-01560-y","volume":"21","author":"X Li","year":"2023","unstructured":"Li, X. et al. Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae). BMC Biol. 21, 56 (2023).","journal-title":"BMC Biol."},{"key":"2442_CR99","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1016\/j.cell.2015.04.004","volume":"161","author":"DG Lupi\u00e1\u00f1ez","year":"2015","unstructured":"Lupi\u00e1\u00f1ez, D. G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene\u2013enhancer interactions. Cell 161, 1012\u20131025 (2015).","journal-title":"Cell"},{"key":"2442_CR100","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34053-7","volume":"13","author":"R Sch\u00f6pflin","year":"2022","unstructured":"Sch\u00f6pflin, R. et al. Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes. Nat. Commun. 13, 6470 (2022).","journal-title":"Nat. Commun."},{"key":"2442_CR101","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/j.tig.2023.10.013","volume":"40","author":"X Lu","year":"2024","unstructured":"Lu, X. & Liu, L. Genome stability from the perspective of telomere length. Trends Genet. 40, 175\u2013186 (2024).","journal-title":"Trends Genet."},{"key":"2442_CR102","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1126\/science.adz8505","volume":"390","author":"M R\u00f6nspies","year":"2025","unstructured":"R\u00f6nspies, M. et al. CRISPR\u2013Cas-mediated heritable chromosome fusions in Arabidopsis. Science 390, 843\u2013848 (2025).","journal-title":"Science"},{"key":"2442_CR103","doi-asserted-by":"publisher","first-page":"2519","DOI":"10.1016\/j.cell.2026.01.026","volume":"189","author":"L Wang","year":"2026","unstructured":"Wang, L. et al. PLANeT: understanding and leveraging the genome of land plants for a sustainable future. Cell 189, 2519\u20132532 (2026).","journal-title":"Cell"},{"key":"2442_CR104","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"2442_CR105","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1038\/nbt.3519","volume":"34","author":"NL Bray","year":"2016","unstructured":"Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525\u2013527 (2016).","journal-title":"Nat. Biotechnol."},{"key":"2442_CR106","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","volume":"37","author":"H Li","year":"2021","unstructured":"Li, H. New strategies to improve minimap2 alignment accuracy. Bioinformatics 37, 4572\u20134574 (2021).","journal-title":"Bioinformatics"},{"key":"2442_CR107","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"2442_CR108","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20236-7","volume":"12","author":"Y Chen","year":"2021","unstructured":"Chen, Y. et al. Efficient assembly of nanopore reads via highly accurate and intact error correction. Nat. Commun. 12, 60 (2021).","journal-title":"Nat. Commun."},{"key":"2442_CR109","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/nbt.1754","volume":"29","author":"JT Robinson","year":"2011","unstructured":"Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24\u201326 (2011).","journal-title":"Nat. Biotechnol."},{"key":"2442_CR110","first-page":"10","volume":"12","author":"S Ou","year":"2019","unstructured":"Ou, S. & Jiang, N. LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. Mob. DNA 12, 10\u201348 (2019).","journal-title":"Mob. DNA"},{"key":"2442_CR111","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1093\/bioinformatics\/bty648","volume":"35","author":"B Langmead","year":"2019","unstructured":"Langmead, B., Wilks, C., Antonescu, V. & Charles, R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics 35, 421\u2013432 (2019).","journal-title":"Bioinformatics"},{"key":"2442_CR112","doi-asserted-by":"publisher","first-page":"W187","DOI":"10.1093\/nar\/gku365","volume":"42","author":"F Ram\u00edrez","year":"2014","unstructured":"Ram\u00edrez, F., D\u00fcndar, F., Diehl, S., Gr\u00fcning, B. A. & Manke, T. DeepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187\u2013W191 (2014).","journal-title":"Nucleic Acids Res."},{"key":"2442_CR113","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).","journal-title":"Genome Biol."},{"key":"2442_CR114","doi-asserted-by":"publisher","first-page":"1752","DOI":"10.1214\/11-AOAS466","volume":"5","author":"Q Li","year":"2011","unstructured":"Li, Q., Brown, J. B., Huang, H. & Bickel, P. J. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5, 1752\u20131779 (2011).","journal-title":"Ann. Appl. Stat."},{"key":"2442_CR115","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-18","volume":"9","author":"D Ellinghaus","year":"2008","unstructured":"Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 9, 18 (2008).","journal-title":"BMC Bioinformatics"},{"key":"2442_CR116","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1104\/pp.17.01310","volume":"176","author":"S Ou","year":"2018","unstructured":"Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiol. 176, 1410\u20131422 (2018).","journal-title":"Plant Physiol."},{"key":"2442_CR117","doi-asserted-by":"publisher","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","volume":"3","author":"T Br\u016fna","year":"2021","unstructured":"Br\u016fna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. 3, lqaa108 (2021).","journal-title":"NAR Genom. Bioinform."},{"key":"2442_CR118","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1101\/gr.6743907","volume":"18","author":"BL Cantarel","year":"2008","unstructured":"Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188\u2013196 (2008).","journal-title":"Genome Res."},{"key":"2442_CR119","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150\u20133152 (2012).","journal-title":"Bioinformatics"},{"key":"2442_CR120","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 1\u201314 (2019).","journal-title":"Genome Biol."},{"key":"2442_CR121","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","unstructured":"Capella-Guti\u00e9rrez, S., Silla-Mart\u00ednez, J. M. & Gabald\u00f3n, T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972\u20131973 (2009).","journal-title":"Bioinformatics"},{"key":"2442_CR122","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamatakis","year":"2014","unstructured":"Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312\u20131313 (2014).","journal-title":"Bioinformatics"},{"key":"2442_CR123","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."},{"key":"2442_CR124","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/s41477-019-0421-0","volume":"5","author":"HT Li","year":"2019","unstructured":"Li, H. T. et al. Origin of angiosperms and the puzzle of the Jurassic gap. Nat. Plants 5, 461\u2013470 (2019).","journal-title":"Nat. Plants"},{"key":"2442_CR125","doi-asserted-by":"publisher","first-page":"2696","DOI":"10.1111\/ddi.13624","volume":"28","author":"Q Zhang","year":"2022","unstructured":"Zhang, Q. et al. New insights into the formation of biodiversity hotspots of the Kenyan flora. Divers. Distrib. 28, 2696\u20132711 (2022).","journal-title":"Divers. Distrib."},{"key":"2442_CR126","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1016\/j.ympev.2011.11.015","volume":"62","author":"G Zecca","year":"2012","unstructured":"Zecca, G. et al. The timing and the mode of evolution of wild grapes (Vitis). Mol. Phylogenet. Evol. 62, 736\u2013747 (2012).","journal-title":"Mol. Phylogenet. Evol."},{"key":"2442_CR127","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1471-2148-12-17","volume":"12","author":"ZL Nie","year":"2012","unstructured":"Nie, Z. L. et al. Evolution of the intercontinental disjunctions in six continents in the Ampelopsis clade of the grape family (Vitaceae). BMC Evol. Biol. 12, 17 (2012).","journal-title":"BMC Evol. Biol."},{"key":"2442_CR128","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.3732\/ajb.1000085","volume":"97","author":"ZL Nie","year":"2010","unstructured":"Nie, Z. L. et al. Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America. Am. J. Bot. 97, 1342\u20131353 (2010).","journal-title":"Am. J. Bot."},{"key":"2442_CR129","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.ympev.2015.10.013","volume":"95","author":"XQ Liu","year":"2016","unstructured":"Liu, X. Q. et al. Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus. Mol. Phylogenet. Evol. 95, 217\u2013228 (2016).","journal-title":"Mol. Phylogenet. Evol."},{"key":"2442_CR130","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1111\/1365-2745.12154","volume":"101","author":"TJ Davies","year":"2013","unstructured":"Davies, T. J. et al. Phylogenetic conservatism in plant phenology. J. Ecol. 101, 1520\u20131530 (2013).","journal-title":"J. Ecol."},{"key":"2442_CR131","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1016\/j.ympev.2013.04.023","volume":"68","author":"L Lu","year":"2013","unstructured":"Lu, L., Wang, W., Chen, Z. & Wen, J. Phylogeny of the non-monophyletic Cayratia Juss. (Vitaceae) and implications for character evolution and biogeography. Mol. Phylogenet. Evol. 68, 502\u2013515 (2013).","journal-title":"Mol. Phylogenet. Evol."},{"key":"2442_CR132","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1111\/nph.13261","volume":"206","author":"Y-H Wang","year":"2015","unstructured":"Wang, Y.-H. et al. Molecular phylogeography and ecological niche modelling of a widespread herbaceous climber, Tetrastigma hemsleyanum (Vitaceae): insights into Plio\u2013Pleistocene range dynamics of evergreen forest in subtropical China. New Phytol. 206, 852\u2013867 (2015).","journal-title":"New Phytol."},{"key":"2442_CR133","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-34630-w","volume":"13","author":"RC Edgar","year":"2022","unstructured":"Edgar, R. C. Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nat. Commun. 13, 6968 (2022).","journal-title":"Nat. Commun."},{"key":"2442_CR134","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"2442_CR135","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"2442_CR136","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"2442_CR137","doi-asserted-by":"publisher","unstructured":"Poplin, R. et al. Scaling accurate genetic variant discovery to tens of thousands of samples. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/201178 (2017).","DOI":"10.1101\/201178"},{"key":"2442_CR138","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":"2442_CR139","doi-asserted-by":"publisher","first-page":"e211","DOI":"10.1002\/imt2.211","volume":"3","author":"H Tang","year":"2024","unstructured":"Tang, H. et al. JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3, e211 (2024).","journal-title":"iMeta"},{"key":"2442_CR140","doi-asserted-by":"publisher","first-page":"2008","DOI":"10.1038\/s41592-024-02430-3","volume":"21","author":"E Garrison","year":"2024","unstructured":"Garrison, E. et al. Building pangenome graphs. Nat. Methods 21, 2008\u20132012 (2024).","journal-title":"Nat. Methods"},{"key":"2442_CR141","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","volume":"617","author":"W-W Liao","year":"2023","unstructured":"Liao, W.-W. et al. A draft human pangenome reference. Nature 617, 312\u2013324 (2023).","journal-title":"Nature"},{"key":"2442_CR142","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"2442_CR143","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02840-6","volume":"23","author":"AC English","year":"2022","unstructured":"English, A. C., Menon, V. K., Gibbs, R. A., Metcalf, G. A. & Sedlazeck, F. J. Truvari: refined structural variant comparison preserves allelic diversity. Genome Biol. 23, 271 (2022).","journal-title":"Genome Biol."},{"key":"2442_CR144","doi-asserted-by":"publisher","first-page":"btae720","DOI":"10.1093\/bioinformatics\/btae720","volume":"40","author":"L Parmigiani","year":"2024","unstructured":"Parmigiani, L., Garrison, E., Stoye, J., Marschall, T. & Doerr, D. Panacus: fast and exact pangenome growth and core size estimation. Bioinformatics 40, btae720 (2024).","journal-title":"Bioinformatics"},{"key":"2442_CR145","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0831-x","volume":"16","author":"N Servant","year":"2015","unstructured":"Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).","journal-title":"Genome Biol."},{"key":"2442_CR146","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/nmeth.2148","volume":"9","author":"M Imakaev","year":"2012","unstructured":"Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999\u20131003 (2012).","journal-title":"Nat. Methods"},{"key":"2442_CR147","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giac061","volume":"11","author":"J Wolff","year":"2022","unstructured":"Wolff, J., Backofen, R. & Gr\u00fcning, B. Loop detection using Hi-C data with HiCExplorer. GigaScience 11, giac061 (2022).","journal-title":"GigaScience"},{"key":"2442_CR148","doi-asserted-by":"publisher","first-page":"e1012067","DOI":"10.1371\/journal.pcbi.1012067","volume":"20","author":"N Abdennur","year":"2024","unstructured":"Abdennur, N. et al. Cooltools: enabling high-resolution Hi-C analysis in Python. PLOS Comput. Biol. 20, e1012067 (2024).","journal-title":"PLOS Comput. Biol."},{"key":"2442_CR149","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.1093\/bioinformatics\/btt730","volume":"30","author":"H Zhao","year":"2014","unstructured":"Zhao, H. et al. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 1006\u20131007 (2014).","journal-title":"Bioinformatics"},{"key":"2442_CR150","doi-asserted-by":"publisher","first-page":"btad014","DOI":"10.1093\/bioinformatics\/btad014","volume":"39","author":"H Li","year":"2023","unstructured":"Li, H. Protein-to-genome alignment with miniprot. Bioinformatics 39, btad014 (2023).","journal-title":"Bioinformatics"},{"key":"2442_CR151","doi-asserted-by":"publisher","unstructured":"Wang, X. Chromosome-level phylogenomics and genome evolution of the grape family. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.33329247 (2026).","DOI":"10.6084\/m9.figshare.33329247"},{"key":"2442_CR152","doi-asserted-by":"publisher","unstructured":"Wang, X. Chromosome-level phylogenomics and genome evolution of the grape family. v3 edn. Zenodo https:\/\/doi.org\/10.5281\/zenodo.18590277 (2025).","DOI":"10.5281\/zenodo.18590277"}],"container-title":["Nature Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41477-026-02442-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41477-026-02442-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41477-026-02442-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T09:01:46Z","timestamp":1792746106000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41477-026-02442-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,23]]},"references-count":152,"alternative-id":["2442"],"URL":"https:\/\/doi.org\/10.1038\/s41477-026-02442-1","relation":{},"ISSN":["2055-0278"],"issn-type":[{"value":"2055-0278","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,23]]},"assertion":[{"value":"29 September 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 October 2026","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","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}]}}