{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,12]],"date-time":"2026-11-12T14:22:20Z","timestamp":1794493340204,"version":"4.9.1"},"reference-count":158,"publisher":"Springer Science and Business Media LLC","issue":"8073","license":[{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2025,7,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Cannabis sativa<\/jats:italic>\n                    is a globally important seed oil, fibre and drug-producing plant species. However, a century of prohibition has severely restricted development of breeding and germplasm resources, leaving potential hemp-based nutritional and fibre applications unrealized. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 144 biological samples including both male (XY) and female (XX) plants. We identified widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Across the ancient heteromorphic X and Y sex chromosomes, we observed a variable boundary at the sex-determining and pseudoautosomal regions as well as genes that exhibit male-biased expression, including genes encoding several key flowering regulators. Conversely, the cannabinoid synthase genes, which are responsible for producing cannabidiol acid and delta-9-tetrahydrocannabinolic acid, contained very low levels of diversity, despite being embedded within a variable region with multiple pseudogenized paralogues, structural variation and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase genes that were associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabivarin and cannabidivarin. We conclude that the\n                    <jats:italic>C. sativa<\/jats:italic>\n                    gene pool remains only partially characterized, the existence of wild relatives in Asia is likely and its potential as a crop species remains largely unrealized.\n                  <\/jats:p>","DOI":"10.1038\/s41586-025-09065-0","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T11:02:31Z","timestamp":1748430151000},"page":"1001-1010","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":56,"title":["Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome"],"prefix":"10.1038","volume":"643","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2032-6078","authenticated-orcid":false,"given":"Ryan C.","family":"Lynch","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3157-4990","authenticated-orcid":false,"given":"Lillian K.","family":"Padgitt-Cobb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea R.","family":"Garfinkel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1665-4343","authenticated-orcid":false,"given":"Brian J.","family":"Knaus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nolan T.","family":"Hartwick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1145-1646","authenticated-orcid":false,"given":"Nicholas","family":"Allsing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony","family":"Aylward","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2232-7488","authenticated-orcid":false,"given":"Philip C.","family":"Bentz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6431-0660","authenticated-orcid":false,"given":"Sarah B.","family":"Carey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allen","family":"Mamerto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justine K.","family":"Kitony","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8913-4678","authenticated-orcid":false,"given":"Kelly","family":"Colt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9349-4325","authenticated-orcid":false,"given":"Emily R.","family":"Murray","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany","family":"Duong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1744-8461","authenticated-orcid":false,"given":"Heidi I.","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2613-1839","authenticated-orcid":false,"given":"Aaron","family":"Trippe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2035-0871","authenticated-orcid":false,"given":"Alex","family":"Harkess","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth","family":"Crawford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Vining","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6272-2875","authenticated-orcid":false,"given":"Todd P.","family":"Michael","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"9065_CR1","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s00334-016-0579-6","volume":"26","author":"T Long","year":"2017","unstructured":"Long, T., Wagner, M., Demske, D., Leipe, C. & Tarasov, P. E. Cannabis in Eurasia: origin of human use and Bronze Age trans-continental connections. Veg. Hist. Archaeobot. 26, 245\u2013258 (2017).","journal-title":"Veg. Hist. Archaeobot."},{"key":"9065_CR2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abg2286","volume":"7","author":"G Ren","year":"2021","unstructured":"Ren, G. et al. Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. Sci. Adv. 7, eabg2286 (2021).","journal-title":"Sci. Adv."},{"key":"9065_CR3","doi-asserted-by":"publisher","first-page":"114114","DOI":"10.1016\/j.jep.2021.114114","volume":"275","author":"Y Bai","year":"2021","unstructured":"Bai, Y. et al. Archaeobotanical evidence of the use of medicinal cannabis in a secular context unearthed from south China. J. Ethnopharmacol. 275, 114114 (2021).","journal-title":"J. Ethnopharmacol."},{"key":"9065_CR4","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1146\/annurev-arplant-081519-040203","volume":"71","author":"I Kovalchuk","year":"2020","unstructured":"Kovalchuk, I. et al. The genomics of cannabis and its close relatives. Annu. Rev. Plant Biol. 71, 713\u2013739 (2020).","journal-title":"Annu. Rev. Plant Biol."},{"key":"9065_CR5","unstructured":"Clarke, R. & Merlin, M. Cannabis: Evolution and Ethnobotany (Univ. of California Press, 2016)."},{"key":"9065_CR6","doi-asserted-by":"crossref","unstructured":"Stoa, R. Craft Weed: Family Farming and the Future of the Marijuana Industry (MIT Press, 2018).","DOI":"10.7551\/mitpress\/11355.001.0001"},{"key":"9065_CR7","first-page":"1","volume":"34","author":"DV Patton","year":"2020","unstructured":"Patton, D. V. A history of United States cannabis law. J. Law Health 34, 1\u201329 (2020).","journal-title":"J. Law Health"},{"key":"9065_CR8","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.drugpo.2011.08.003","volume":"23","author":"D Bewley-Taylor","year":"2012","unstructured":"Bewley-Taylor, D. & Jelsma, M. Regime change: re-visiting the 1961 Single Convention on Narcotic Drugs. Int. J. Drug Policy 23, 72\u201381 (2012).","journal-title":"Int. J. Drug Policy"},{"key":"9065_CR9","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1039\/C6NP00074F","volume":"33","author":"LO Hanu\u0161","year":"2016","unstructured":"Hanu\u0161, L. O., Meyer, S. M., Mu\u00f1oz, E., Taglialatela-Scafati, O. & Appendino, G. Phytocannabinoids: a unified critical inventory. Nat. Prod. Rep. 33, 1357\u20131392 (2016).","journal-title":"Nat. Prod. Rep."},{"key":"9065_CR10","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.1056\/NEJMoa1611618","volume":"376","author":"O Devinsky","year":"2017","unstructured":"Devinsky, O. et al. Trial of cannabidiol for drug-resistant seizures in the Dravet syndrome. N. Engl. J. Med. 376, 2011\u20132020 (2017).","journal-title":"N. Engl. J. Med."},{"key":"9065_CR11","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1111\/nph.17243","volume":"230","author":"CJ Grassa","year":"2021","unstructured":"Grassa, C. J. et al. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana. New Phytol. 230, 1665\u20131679 (2021).","journal-title":"New Phytol."},{"key":"9065_CR12","doi-asserted-by":"publisher","unstructured":"McKernan, K. J. et al. Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2020.01.03.894428 (2020).","DOI":"10.1101\/2020.01.03.894428"},{"key":"9065_CR13","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/s41438-020-0295-3","volume":"7","author":"S Gao","year":"2020","unstructured":"Gao, S. et al. A high-quality reference genome of wild Cannabis sativa. Hortic. Res. 7, 73 (2020).","journal-title":"Hortic. Res."},{"key":"9065_CR14","doi-asserted-by":"publisher","unstructured":"Braich, S., Baillie, R. C., Spangenberg, G. C. & Cogan, N. O. I. A new and improved genome sequence of Cannabis sativa. GigaByte https:\/\/doi.org\/10.46471\/gigabyte.10 (2020).","DOI":"10.46471\/gigabyte.10"},{"key":"9065_CR15","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-10-r102","volume":"12","author":"H van Bakel","year":"2011","unstructured":"van Bakel, H. et al. The draft genome and transcriptome of Cannabis sativa. Genome Biol. 12, R102 (2011).","journal-title":"Genome Biol."},{"key":"9065_CR16","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1101\/gr.242594.118","volume":"29","author":"KU Laverty","year":"2019","unstructured":"Laverty, K. U. et al. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC\/CBD acid synthase loci. Genome Res. 29, 146\u2013156 (2019).","journal-title":"Genome Res."},{"key":"9065_CR17","doi-asserted-by":"publisher","first-page":"573299","DOI":"10.3389\/fpls.2020.573299","volume":"11","author":"G Barcaccia","year":"2020","unstructured":"Barcaccia, G. et al. Potentials and challenges of genomics for breeding cannabis cultivars. Front. Plant Sci. 11, 573299 (2020).","journal-title":"Front. Plant Sci."},{"key":"9065_CR18","doi-asserted-by":"publisher","first-page":"81","DOI":"10.3897\/phytokeys.144.46700","volume":"144","author":"JM McPartland","year":"2020","unstructured":"McPartland, J. M. & Small, E. A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives. PhytoKeys 144, 81\u2013112 (2020).","journal-title":"PhytoKeys"},{"key":"9065_CR19","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","volume":"31","author":"FA Sim\u00e3o","year":"2015","unstructured":"Sim\u00e3o, 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":"9065_CR20","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/s41587-023-01793-w","volume":"42","author":"G Hickey","year":"2024","unstructured":"Hickey, G. et al. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat. Biotechnol. 42, 663\u2013673 (2024).","journal-title":"Nat. Biotechnol."},{"key":"9065_CR21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad621","volume":"39","author":"AJ Aylward","year":"2023","unstructured":"Aylward, A. J., Petrus, S., Mamerto, A., Hartwick, N. T. & Michael, T. P. PanKmer: k-mer-based and reference-free pangenome analysis. Bioinformatics 39, btad621 (2023).","journal-title":"Bioinformatics"},{"key":"9065_CR22","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":"9065_CR23","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/s12229-017-9187-0","volume":"83","author":"JM McPartland","year":"2017","unstructured":"McPartland, J. M. & Guy, G. W. Models of cannabis taxonomy, cultural bias, and conflicts between scientific and vernacular names. Bot. Rev. 83, 327\u2013381 (2017).","journal-title":"Bot. Rev."},{"key":"9065_CR24","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2105431118","volume":"118","author":"Q Qiao","year":"2021","unstructured":"Qiao, Q. et al. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proc. Natl Acad. Sci. USA 118, e2105431118 (2021).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"9065_CR25","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1111\/tpj.16622","volume":"118","author":"C Li","year":"2024","unstructured":"Li, C., Lin, H., Debernardi, J. M., Zhang, C. & Dubcovsky, J. GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1. Plant J. 118, 519\u2013533 (2024).","journal-title":"Plant J."},{"key":"9065_CR26","doi-asserted-by":"publisher","DOI":"10.1126\/science.abc9141","volume":"372","author":"G Steed","year":"2021","unstructured":"Steed, G., Ramirez, D. C., Hannah, M. A. & Webb, A. A. R. Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 372, eabc9141 (2021).","journal-title":"Science"},{"key":"9065_CR27","first-page":"66","volume":"2","author":"E de Meijer","year":"1995","unstructured":"de Meijer, E. Fibre hemp cultivars: a survey oforigin, ancestry,availability and brief agronomic characteristics. J. Int. Hemp Assoc. 2, 66\u201373 (1995).","journal-title":"J. Int. Hemp Assoc."},{"key":"9065_CR28","doi-asserted-by":"crossref","unstructured":"Westergaard. M. in Advances in Genetics, Vol. 9 (ed. Demerec, M.) 217\u2013281 (Academic Press, 1958).","DOI":"10.1016\/S0065-2660(08)60163-7"},{"key":"9065_CR29","doi-asserted-by":"publisher","unstructured":"Carey, S. B. et al. The evolution of heteromorphic sex chromosomes in plants. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.12.09.627636 (2024).","DOI":"10.1101\/2024.12.09.627636"},{"key":"9065_CR30","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1089\/can.2018.0039","volume":"3","author":"JM McPartland","year":"2018","unstructured":"McPartland, J. M. Cannabis systematics at the levels of family, genus, and species. Cannabis Cannabinoid Res. 3, 203\u2013212 (2018).","journal-title":"Cannabis Cannabinoid Res."},{"key":"9065_CR31","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1111\/nph.17456","volume":"231","author":"D Prentout","year":"2021","unstructured":"Prentout, D. et al. Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes. New Phytol. 231, 1599\u20131611 (2021).","journal-title":"New Phytol."},{"key":"9065_CR32","doi-asserted-by":"publisher","first-page":"569958","DOI":"10.3389\/fpls.2020.569958","volume":"11","author":"J Petit","year":"2020","unstructured":"Petit, J., Salentijn, E. M. J., Paulo, M.-J., Denneboom, C. & Trindade, L. M. Genetic architecture of flowering time and sex determination in hemp (Cannabis sativa L.): a genome-wide association study. Front. Plant Sci. 11, 569958 (2020).","journal-title":"Front. Plant Sci."},{"key":"9065_CR33","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1038\/sj.hdy.6800697","volume":"95","author":"D Charlesworth","year":"2005","unstructured":"Charlesworth, D., Charlesworth, B. & Marais, G. Steps in the evolution of heteromorphic sex chromosomes. Heredity 95, 118\u2013128 (2005).","journal-title":"Heredity"},{"key":"9065_CR34","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.3390\/ijms26031165","volume":"26","author":"GM Stack","year":"2025","unstructured":"Stack, G. M. et al. Comparison of recombination rate, reference bias, and unique pangenomic haplotypes in Cannabis sativa using seven de novo genome assemblies. Int. J. Mol. Sci. 26, 1165 (2025).","journal-title":"Int. J. Mol. Sci."},{"key":"9065_CR35","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1105\/tpc.16.00568","volume":"29","author":"C Lu","year":"2017","unstructured":"Lu, C. et al. Phosphorylation of SPT5 by CDKD;2 is required for VIP5 recruitment and normal flowering in Arabidopsis thaliana. Plant Cell 29, 277\u2013291 (2017).","journal-title":"Plant Cell"},{"key":"9065_CR36","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1007\/s00438-015-1000-3","volume":"290","author":"FM Lappin","year":"2015","unstructured":"Lappin, F. M. et al. A polymorphic pseudoautosomal boundary in the Carica papaya sex chromosomes. Mol. Genet. Genomics 290, 1511\u20131522 (2015).","journal-title":"Mol. Genet. Genomics"},{"key":"9065_CR37","doi-asserted-by":"publisher","first-page":"207","DOI":"10.5586\/asbp.2006.024","volume":"75","author":"A Grabowska-Joachimiak","year":"2006","unstructured":"Grabowska-Joachimiak, A., \u015aliwi\u0144ska, E., Pigu\u0142a, M., Skomra, U. & Joachimiak, A. J. Genome size in Humulus lupulus L. and H. japonicus Siebold and Zucc. (Cannabaceae). Acta Soc. Bot. Pol. 75, 207\u2013214 (2006).","journal-title":"Acta Soc. Bot. Pol."},{"key":"9065_CR38","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1101\/gr.1466204","volume":"14","author":"J Ma","year":"2004","unstructured":"Ma, J., Devos, K. M. & Bennetzen, J. L. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14, 860\u2013869 (2004).","journal-title":"Genome Res."},{"key":"9065_CR39","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1016\/j.molcel.2019.10.011","volume":"77","author":"J Choi","year":"2020","unstructured":"Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D. & Zilberman, D. DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts. Mol. Cell 77, 310\u2013323.e7 (2020).","journal-title":"Mol. Cell"},{"key":"9065_CR40","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1038\/s41559-022-01890-0","volume":"6","author":"OS Harringmeyer","year":"2022","unstructured":"Harringmeyer, O. S. & Hoekstra, H. E. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat. Ecol. Evol. 6, 1965\u20131979 (2022).","journal-title":"Nat. Ecol. Evol."},{"key":"9065_CR41","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1093\/evolut\/qpad027","volume":"77","author":"K Hirabayashi","year":"2023","unstructured":"Hirabayashi, K. & Owens, G. L. The rate of chromosomal inversion fixation in plant genomes is highly variable. Evolution 77, 1117\u20131130 (2023).","journal-title":"Evolution"},{"key":"9065_CR42","first-page":"733","volume":"132","author":"I Gabur","year":"2019","unstructured":"Gabur, I., Chawla, H. S., Snowdon, R. J. & Parkin, I. A. P. Connecting genome structural variation with complex traits in crop plants. Z\u00fcchter Genet. Breed. Res. 132, 733\u2013750 (2019).","journal-title":"Z\u00fcchter Genet. Breed. Res."},{"key":"9065_CR43","doi-asserted-by":"publisher","first-page":"1839","DOI":"10.1016\/j.cub.2018.04.072","volume":"28","author":"P Jay","year":"2018","unstructured":"Jay, P. et al. Supergene evolution triggered by the introgression of a chromosomal inversion. Curr. Biol. 28, 1839\u20131845.e3 (2018).","journal-title":"Curr. Biol."},{"key":"9065_CR44","doi-asserted-by":"publisher","first-page":"991680","DOI":"10.3389\/fpls.2022.991680","volume":"13","author":"JA Toth","year":"2022","unstructured":"Toth, J. A., Stack, G. M., Carlson, C. H. & Smart, L. B. Identification and mapping of major-effect flowering time loci Autoflower1 and Early1 in Cannabis sativa L. Front. Plant Sci. 13, 991680 (2022).","journal-title":"Front. Plant Sci."},{"key":"9065_CR45","doi-asserted-by":"publisher","first-page":"16469","DOI":"10.1073\/pnas.1106212108","volume":"108","author":"RL Murphy","year":"2011","unstructured":"Murphy, R. L. et al. Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. Proc. Natl Acad. Sci. USA 108, 16469\u201316474 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"9065_CR46","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1093\/pcp\/pcy215","volume":"60","author":"M-W Li","year":"2019","unstructured":"Li, M.-W., Liu, W., Lam, H.-M. & Gendron, J. M. Characterization of two growth period QTLs reveals modification of PRR3 genes during soybean domestication. Plant Cell Physiol. 60, 407\u2013420 (2019).","journal-title":"Plant Cell Physiol."},{"key":"9065_CR47","doi-asserted-by":"publisher","first-page":"1933","DOI":"10.1038\/s41559-024-02514-5","volume":"8","author":"JR Whiting","year":"2024","unstructured":"Whiting, J. R. et al. The genetic architecture of repeated local adaptation to climate in distantly related plants. Nat. Ecol. Evol. 8, 1933\u20131947 (2024).","journal-title":"Nat. Ecol. Evol."},{"key":"9065_CR48","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1038\/s41586-020-2467-6","volume":"584","author":"M Todesco","year":"2020","unstructured":"Todesco, M. et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602\u2013607 (2020).","journal-title":"Nature"},{"key":"9065_CR49","doi-asserted-by":"publisher","unstructured":"Andre, C. M. et al. Unique bibenzyl cannabinoids in the liverwort Radula marginata: parallels with Cannabis chemistry. New Phytol. https:\/\/doi.org\/10.1111\/nph.20349 (2024).","DOI":"10.1111\/nph.20349"},{"key":"9065_CR50","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evab130","volume":"13","author":"R van Velzen","year":"2021","unstructured":"van Velzen, R. & Schranz, M. E. Origin and evolution of the cannabinoid oxidocyclase gene family. Genome Biol. Evol. 13, evab130 (2021).","journal-title":"Genome Biol. Evol."},{"key":"9065_CR51","doi-asserted-by":"publisher","first-page":"e0267498","DOI":"10.1371\/journal.pone.0267498","volume":"17","author":"CJ Smith","year":"2022","unstructured":"Smith, C. J., Vergara, D., Keegan, B. & Jikomes, N. The phytochemical diversity of commercial Cannabis in the United States. PLoS ONE 17, e0267498 (2022).","journal-title":"PLoS ONE"},{"key":"9065_CR52","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1007\/s10681-016-1721-3","volume":"210","author":"EPM de Meijer","year":"2016","unstructured":"de Meijer, E. P. M. & Hammond, K. M. The inheritance of chemical phenotype in Cannabis sativa L. (V): regulation of the propyl-\/pentyl cannabinoid ratio, completion of a genetic model. Euphytica 210, 291\u2013307 (2016).","journal-title":"Euphytica"},{"key":"9065_CR53","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.neuropharm.2018.07.029","volume":"140","author":"D Vigli","year":"2018","unstructured":"Vigli, D. et al. Chronic treatment with the phytocannabinoid Cannabidivarin (CBDV) rescues behavioural alterations and brain atrophy in a mouse model of Rett syndrome. Neuropharmacology 140, 121\u2013129 (2018).","journal-title":"Neuropharmacology"},{"key":"9065_CR54","doi-asserted-by":"publisher","first-page":"18643","DOI":"10.1038\/s41598-020-75271-7","volume":"10","author":"MT Welling","year":"2020","unstructured":"Welling, M. T. et al. An extreme-phenotype genome\u2010wide association study identifies candidate cannabinoid pathway genes in Cannabis. Sci. Rep. 10, 18643 (2020).","journal-title":"Sci. Rep."},{"key":"9065_CR55","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1007\/s11103-013-0151-z","volume":"84","author":"IP Pulsifer","year":"2014","unstructured":"Pulsifer, I. P. et al. Acyl-lipid thioesterase1-4 from Arabidopsis thaliana form a novel family of fatty acyl-acyl carrier protein thioesterases with divergent expression patterns and substrate specificities. Plant Mol. Biol. 84, 549\u2013563 (2014).","journal-title":"Plant Mol. Biol."},{"key":"9065_CR56","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1002\/lipd.12226","volume":"55","author":"RS Kalinger","year":"2020","unstructured":"Kalinger, R. S., Pulsifer, I. P., Hepworth, S. R. & Rowland, O. Fatty acyl synthetases and thioesterases in plant lipid metabolism: diverse functions and biotechnological applications. Lipids 55, 435\u2013455 (2020).","journal-title":"Lipids"},{"key":"9065_CR57","doi-asserted-by":"publisher","first-page":"1601","DOI":"10.1002\/jps.2600621005","volume":"62","author":"CE Turner","year":"1973","unstructured":"Turner, C. E. et al. Constituents of Cannabis sativa L. IV. Stability of cannabinoids in stored plant material. J. Pharm. Sci. 62, 1601\u20131605 (1973).","journal-title":"J. Pharm. Sci."},{"key":"9065_CR58","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1007\/s10681-015-1585-y","volume":"208","author":"MT Welling","year":"2016","unstructured":"Welling, M. T., Liu, L., Shapter, T., Raymond, C. A. & King, G. J. Characterisation of cannabinoid composition in a diverse Cannabis sativa L. germplasm collection. Euphytica 208, 463\u2013475 (2016).","journal-title":"Euphytica"},{"key":"9065_CR59","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170\u2013175 (2021).","journal-title":"Nat. Methods"},{"key":"9065_CR60","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":"9065_CR61","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":"9065_CR62","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":"9065_CR63","doi-asserted-by":"publisher","unstructured":"Krueger, F. et al. FelixKrueger\/TrimGalore: v0.6.10. Zenodo https:\/\/doi.org\/10.5281\/zenodo.7598955 (2023).","DOI":"10.5281\/zenodo.7598955"},{"key":"9065_CR64","doi-asserted-by":"publisher","unstructured":"Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. Preprint at https:\/\/doi.org\/10.48550\/arXiv.1207.3907 (2012).","DOI":"10.48550\/arXiv.1207.3907"},{"key":"9065_CR65","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":"9065_CR66","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":"9065_CR67","doi-asserted-by":"publisher","first-page":"228","DOI":"10.3390\/genes12020228","volume":"12","author":"AR Garfinkel","year":"2021","unstructured":"Garfinkel, A. R., Otten, M. & Crawford, S. SNP in potentially defunct tetrahydrocannabinolic acid synthase is a marker for cannabigerolic acid dominance in Cannabis sativa L. Genes 12, 228 (2021).","journal-title":"Genes"},{"key":"9065_CR68","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417\u2013419 (2017).","journal-title":"Nat. Methods"},{"key":"9065_CR69","doi-asserted-by":"publisher","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","volume":"40","author":"Y Wang","year":"2012","unstructured":"Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR70","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","volume":"9","author":"Hunter","year":"2007","unstructured":"Hunter, Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90\u201395 (2007).","journal-title":"Comput. Sci. Eng."},{"key":"9065_CR71","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","volume":"17","author":"P Virtanen","year":"2020","unstructured":"Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261\u2013272 (2020).","journal-title":"Nat. Methods"},{"key":"9065_CR72","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","volume":"585","author":"CR Harris","year":"2020","unstructured":"Harris, C. R. et al. Array programming with NumPy. Nature 585, 357\u2013362 (2020).","journal-title":"Nature"},{"key":"9065_CR73","doi-asserted-by":"publisher","unstructured":"Alexa, A. & Rahnenf\u00fchrer, J. topGO: enrichment analysis for Gene Ontology. https:\/\/doi.org\/10.18129\/B9.bioc.topGO, R package version 2.59.0 (2024).","DOI":"10.18129\/B9.bioc.topGO"},{"key":"9065_CR74","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1101\/gr.279091.124","volume":"34","author":"T Denyer","year":"2024","unstructured":"Denyer, T. et al. Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana. Genome Res. 34, 1106\u20131120 (2024).","journal-title":"Genome Res."},{"key":"9065_CR75","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"9065_CR76","doi-asserted-by":"publisher","unstructured":"Schalamun, M. High molecular weight gDNA extraction after Mayjonade et al. optimised for eucalyptus for nanopore sequencing. Protocols.io https:\/\/doi.org\/10.17504\/protocols.io.i6vche6 (2017).","DOI":"10.17504\/protocols.io.i6vche6"},{"key":"9065_CR77","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1038\/nmeth.4035","volume":"13","author":"C-S Chin","year":"2016","unstructured":"Chin, C.-S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050\u20131054 (2016).","journal-title":"Nat. Methods"},{"key":"9065_CR78","doi-asserted-by":"publisher","first-page":"1291","DOI":"10.1101\/gr.263566.120","volume":"30","author":"S Nurk","year":"2020","unstructured":"Nurk, S. et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res. 30, 1291\u20131305 (2020).","journal-title":"Genome Res."},{"key":"9065_CR79","doi-asserted-by":"publisher","first-page":"27","DOI":"10.21105\/joss.00027","volume":"1","author":"C Titus Brown","year":"2016","unstructured":"Titus Brown, C. & Irber, L. sourmash: a library for MinHash sketching of DNA. J. Open Source Softw. 1, 27 (2016).","journal-title":"J. Open Source Softw."},{"key":"9065_CR80","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7","volume":"23","author":"M Alonge","year":"2022","unstructured":"Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 23, 258 (2022).","journal-title":"Genome Biol."},{"key":"9065_CR81","doi-asserted-by":"publisher","unstructured":"Kurtzer, G. M. et al. Hpcng\/singularity: Singularity 3.7.1. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.4435194 (2021).","DOI":"10.5281\/ZENODO.4435194"},{"key":"9065_CR82","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/nbt.4227","volume":"36","author":"E Garrison","year":"2018","unstructured":"Garrison, E. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat. Biotechnol. 36, 875\u2013879 (2018).","journal-title":"Nat. Biotechnol."},{"key":"9065_CR83","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":"9065_CR84","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","volume":"35","author":"P Di Tommaso","year":"2017","unstructured":"Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316\u2013319 (2017).","journal-title":"Nat. Biotechnol."},{"key":"9065_CR85","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae609","volume":"40","author":"S Heumos","year":"2024","unstructured":"Heumos, S. et al. Cluster-efficient pangenome graph construction with nf-core\/pangenome. Bioinformatics 40, btae609 (2024).","journal-title":"Bioinformatics"},{"key":"9065_CR86","doi-asserted-by":"publisher","unstructured":"Heumos, S. et al. Nf-core\/pangenome: Pangenome 1.1.2 - canguro. Zenodo https:\/\/doi.org\/10.5281\/ZENODO.10869589 (2024).","DOI":"10.5281\/ZENODO.10869589"},{"key":"9065_CR87","doi-asserted-by":"publisher","DOI":"10.1126\/science.abg8871","volume":"374","author":"J Sir\u00e9n","year":"2021","unstructured":"Sir\u00e9n, J. et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science 374, abg8871 (2021).","journal-title":"Science"},{"key":"9065_CR88","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-1941-7","volume":"21","author":"G Hickey","year":"2020","unstructured":"Hickey, G. et al. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol. 21, 35 (2020).","journal-title":"Genome Biol."},{"key":"9065_CR89","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":"9065_CR90","doi-asserted-by":"publisher","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, 238 (2019).","journal-title":"Genome Biol."},{"key":"#cr-split#-9065_CR91.1","unstructured":"Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0. 2013\u22122015"},{"key":"#cr-split#-9065_CR91.2","unstructured":"https:\/\/www.repeatmasker.org\/ (2015)."},{"key":"9065_CR92","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1186\/s12859-021-04482-0","volume":"22","author":"L Gabriel","year":"2021","unstructured":"Gabriel, L., Hoff, K. J., Br\u016fna, T., Borodovsky, M. & Stanke, M. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566 (2021).","journal-title":"BMC Bioinformatics"},{"key":"9065_CR93","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907\u2013915 (2019).","journal-title":"Nat. Biotechnol."},{"key":"9065_CR94","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":"9065_CR95","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra, C. P., Hern\u00e1ndez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825\u20135829 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"9065_CR96","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1093\/molbev\/msx319","volume":"35","author":"RM Waterhouse","year":"2018","unstructured":"Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543\u2013548 (2018).","journal-title":"Mol. Biol. Evol."},{"key":"9065_CR97","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1905-y","volume":"20","author":"S Ou","year":"2019","unstructured":"Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).","journal-title":"Genome Biol."},{"key":"9065_CR98","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1911-0","volume":"20","author":"M Goel","year":"2019","unstructured":"Goel, M., Sun, H., Jiao, W.-B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277 (2019).","journal-title":"Genome Biol."},{"key":"9065_CR99","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1093\/bioinformatics\/btac196","volume":"38","author":"M Goel","year":"2022","unstructured":"Goel, M. & Schneeberger, K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38, 2922\u20132926 (2022).","journal-title":"Bioinformatics"},{"key":"9065_CR100","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":"9065_CR101","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1038\/nature15714","volume":"527","author":"R VanBuren","year":"2015","unstructured":"VanBuren, R. et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527, 508\u2013511 (2015).","journal-title":"Nature"},{"key":"9065_CR102","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573\u2013580 (1999).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR103","doi-asserted-by":"publisher","unstructured":"Colt, K. et al. Telomere length in plants estimated with long read sequencing. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2024.03.27.586973 (2024).","DOI":"10.1101\/2024.03.27.586973"},{"key":"9065_CR104","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/hdy.2015.75","volume":"115","author":"A Garcia-Cisneros","year":"2015","unstructured":"Garcia-Cisneros, A. et al. Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina. Heredity 115, 480 (2015).","journal-title":"Heredity"},{"key":"9065_CR105","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-1-r10","volume":"14","author":"DP Melters","year":"2013","unstructured":"Melters, D. P. et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 14, R10 (2013).","journal-title":"Genome Biol."},{"key":"9065_CR106","doi-asserted-by":"publisher","first-page":"e85118","DOI":"10.1371\/journal.pone.0085118","volume":"9","author":"MG Divashuk","year":"2014","unstructured":"Divashuk, M. G., Alexandrov, O. S., Razumova, O. V., Kirov, I. V. & Karlov, G. I, Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system. PLoS ONE 9, e85118 (2014).","journal-title":"PLoS ONE"},{"key":"9065_CR107","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).","journal-title":"Mol. Biol. Evol."},{"key":"9065_CR108","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1111\/1755-0998.12549","volume":"17","author":"BJ Knaus","year":"2017","unstructured":"Knaus, B. J. & Gr\u00fcnwald, N. J. vcfr: a package to manipulate and visualize variant call format data in R. Mol. Ecol. Resour. 17, 44\u201353 (2017).","journal-title":"Mol. Ecol. Resour."},{"key":"9065_CR109","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/j.1469-1809.1949.tb02451.x","volume":"15","author":"S Wright","year":"1951","unstructured":"Wright, S. The genetical structure of populations. Ann. Eugen. 15, 323\u2013354 (1951).","journal-title":"Ann. Eugen."},{"key":"9065_CR110","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","volume":"11","author":"W Shen","year":"2016","unstructured":"Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation. PLoS ONE 11, e0163962 (2016).","journal-title":"PLoS ONE"},{"key":"9065_CR111","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10931-w","volume":"25","author":"H Kaur","year":"2024","unstructured":"Kaur, H., Shannon, L. M. & Samac, D. A. A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study. BMC Genomics 25, 1022 (2024).","journal-title":"BMC Genomics"},{"key":"9065_CR112","doi-asserted-by":"publisher","first-page":"1483","DOI":"10.1093\/oxfordjournals.molbev.a026248","volume":"17","author":"MA Koch","year":"2000","unstructured":"Koch, M. A., Haubold, B. & Mitchell-Olds, T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17, 1483\u20131498 (2000).","journal-title":"Mol. Biol. Evol."},{"key":"9065_CR113","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","volume":"290","author":"M Lynch","year":"2000","unstructured":"Lynch, M. & Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science 290, 1151\u20131155 (2000).","journal-title":"Science"},{"key":"9065_CR114","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":"9065_CR115","first-page":"e126","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":"9065_CR116","doi-asserted-by":"publisher","first-page":"R79","DOI":"10.1186\/gb-2004-5-10-r79","volume":"5","author":"V Pereira","year":"2004","unstructured":"Pereira, V. Insertion bias and purifying selection of retrotransposons in the Arabidopsis thaliana genome. Genome Biol. 5, R79 (2004).","journal-title":"Genome Biol."},{"key":"9065_CR117","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02546-5","volume":"9","author":"R VanBuren","year":"2018","unstructured":"VanBuren, R. et al. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nat. Commun. 9, 13 (2018).","journal-title":"Nat. Commun."},{"key":"9065_CR118","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.ygeno.2017.05.008","volume":"109","author":"G Karak\u00fclah","year":"2017","unstructured":"Karak\u00fclah, G. & Suner, A. PlanTEnrichment: a tool for enrichment analysis of transposable elements in plants. Genomics 109, 336\u2013340 (2017).","journal-title":"Genomics"},{"key":"9065_CR119","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289\u2013300 (1995).","journal-title":"J. R. Stat. Soc."},{"key":"9065_CR120","doi-asserted-by":"publisher","unstructured":"Seabold, S. & Perktold, J. Statsmodels: econometric and statistical modeling with Python. In Proc. 9th Python in Science Conference https:\/\/doi.org\/10.25080\/Majora-92bf1922-011 (SciPy, 2010).","DOI":"10.25080\/Majora-92bf1922-011"},{"key":"9065_CR121","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"9065_CR122","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1093\/bioinformatics\/bts277","volume":"28","author":"S Neph","year":"2012","unstructured":"Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919\u20131920 (2012).","journal-title":"Bioinformatics"},{"key":"9065_CR123","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","volume":"5","author":"MN Price","year":"2010","unstructured":"Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2\u2014approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).","journal-title":"PLoS ONE"},{"key":"9065_CR124","unstructured":"Rambaut, A. FigTree, version 1.4; http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/ (2012)."},{"key":"9065_CR125","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":"9065_CR126","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1126\/science.aaz1776","volume":"369","author":"GTEx Consortium.","year":"2020","unstructured":"GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369, 1318\u20131330 (2020).","journal-title":"Science"},{"key":"9065_CR127","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/0022-2836(87)90689-9","volume":"196","author":"M Gardiner-Garden","year":"1987","unstructured":"Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261\u2013282 (1987).","journal-title":"J. Mol. Biol."},{"key":"9065_CR128","doi-asserted-by":"publisher","first-page":"19359","DOI":"10.1073\/pnas.1921719117","volume":"117","author":"W Zhou","year":"2020","unstructured":"Zhou, W., Liang, G., Molloy, P. L. & Jones, P. A. DNA methylation enables transposable element-driven genome expansion. Proc. Natl Acad. Sci. USA 117, 19359\u201319366 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"9065_CR129","doi-asserted-by":"publisher","first-page":"vbaf009","DOI":"10.1093\/bioadv\/vbaf009","volume":"5","author":"NT Hartwick","year":"2025","unstructured":"Hartwick, N. T. & Michael, T. P. OrthoBrowser: gene family analysis and visualization. Bioinformatics Adv. 5, vbaf009 (2025).","journal-title":"Bioinformatics Adv."},{"key":"9065_CR130","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.plrev.2004.01.002","volume":"1","author":"C Adami","year":"2004","unstructured":"Adami, C. Information theory in molecular biology. Phys. Life Rev. 1, 3\u201322 (2004).","journal-title":"Phys. Life Rev."},{"key":"9065_CR131","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.78526","volume":"11","author":"JT Lovell","year":"2022","unstructured":"Lovell, J. T. et al. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. eLife 11, e78526 (2022).","journal-title":"eLife"},{"key":"9065_CR132","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. http:\/\/www.R-project.org\/ (R Foundation for Statistical Computing, 2013)."},{"key":"9065_CR133","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":"9065_CR134","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1534\/genetics.118.301747","volume":"211","author":"H Li","year":"2019","unstructured":"Li, H. & Ralph, P. Local PCA shows how the effect of population structure differs along the genome. Genetics 211, 289\u2013304 (2019).","journal-title":"Genetics"},{"key":"9065_CR135","doi-asserted-by":"publisher","first-page":"D1483","DOI":"10.1093\/nar\/gkab1087","volume":"50","author":"J Calle Garc\u00eda","year":"2022","unstructured":"Calle Garc\u00eda, J. et al. PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process. Nucleic Acids Res. 50, D1483\u2013D1490 (2022).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR136","doi-asserted-by":"publisher","unstructured":"Mihalyov, P. D. & Garfinkel, A. R. Discovery and genetic mapping of PM1, a powdery mildew resistance gene in Cannabis sativa L. Front. Agron. https:\/\/doi.org\/10.3389\/fagro.2021.720215 (2021).","DOI":"10.3389\/fagro.2021.720215"},{"key":"9065_CR137","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389\u20133402 (1997).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR138","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1093\/protein\/12.2.85","volume":"12","author":"B Rost","year":"1999","unstructured":"Rost, B. Twilight zone of protein sequence alignments. Protein Eng. 12, 85\u201394 (1999).","journal-title":"Protein Eng."},{"key":"9065_CR139","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-57805-1","volume":"10","author":"H-C Zhou","year":"2020","unstructured":"Zhou, H.-C., Shamala, L. F., Yi, X.-K., Yan, Z. & Wei, S. Analysis of terpene synthase family genes in Camellia sinensis with an emphasis on abiotic stress conditions. Sci. Rep. 10, 933 (2020).","journal-title":"Sci. Rep."},{"key":"9065_CR140","doi-asserted-by":"publisher","first-page":"D290","DOI":"10.1093\/nar\/gkr1065","volume":"40","author":"M Punta","year":"2012","unstructured":"Punta, M. et al. The Pfam protein families database. Nucleic Acids Res. 40, D290\u2013D301 (2012).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR141","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).","journal-title":"PLoS Comput. Biol."},{"key":"9065_CR142","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1104\/pp.18.01506","volume":"180","author":"JJ Zager","year":"2019","unstructured":"Zager, J. J., Lange, I., Srividya, N., Smith, A. & Lange, B. M. Gene networks underlying cannabinoid and terpenoid accumulation in cannabis. Plant Physiol. 180, 1877\u20131897 (2019).","journal-title":"Plant Physiol."},{"key":"9065_CR143","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1111\/j.1365-313X.2012.04942.x","volume":"70","author":"H Jin","year":"2012","unstructured":"Jin, H., Song, Z. & Nikolau, B. J. Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development. Plant J. 70, 1015\u20131032 (2012).","journal-title":"Plant J."},{"key":"9065_CR144","unstructured":"Booth, J. Terpene and isoprenoid biosynthesis in Cannabis sativa. PhD thesis, Univ. of British Columbia (2020)."},{"key":"9065_CR145","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","volume":"18","author":"B Buchfink","year":"2021","unstructured":"Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366\u2013368 (2021).","journal-title":"Nat. Methods"},{"key":"9065_CR146","unstructured":"Edgar, R. Usearch. OSTI.gov https:\/\/www.osti.gov\/biblio\/1137186 (2010)."},{"key":"9065_CR147","doi-asserted-by":"publisher","first-page":"W7","DOI":"10.1093\/nar\/gkq291","volume":"38","author":"F Abascal","year":"2010","unstructured":"Abascal, F., Zardoya, R. & Telford, M. J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38, W7\u2013W13 (2010).","journal-title":"Nucleic Acids Res."},{"key":"9065_CR148","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","volume":"38","author":"K Tamura","year":"2021","unstructured":"Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022\u20133027 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"9065_CR149","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/j.gpb.2021.08.005","volume":"19","author":"J Wang","year":"2021","unstructured":"Wang, J. & Zhang, Z. GAPIT Version 3: boosting power and accuracy for genomic association and prediction. Genomics Proteomics Bioinformatics 19, 629\u2013640 (2021).","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"9065_CR150","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","volume":"28","author":"M Kearse","year":"2012","unstructured":"Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647\u20131649 (2012).","journal-title":"Bioinformatics"},{"key":"9065_CR151","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1101\/gr.251207.119","volume":"30","author":"D Prentout","year":"2020","unstructured":"Prentout, D. et al. An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa. Genome Res. 30, 164\u2013172 (2020).","journal-title":"Genome Res."},{"key":"9065_CR152","unstructured":"Lynch, R. Cannabis_Pangenome. Figshare https:\/\/figshare.com\/projects\/Cannabis_Pangenome\/205555 (2024)."},{"key":"9065_CR153","doi-asserted-by":"publisher","unstructured":"Lynch, R. Cannabis pangenome. Figshare https:\/\/doi.org\/10.25452\/figshare.plus.c.7248427.v1 (2024).","DOI":"10.25452\/figshare.plus.c.7248427.v1"},{"key":"9065_CR154","doi-asserted-by":"publisher","unstructured":"Lynch, R. et al. Pangenome metadata and statistics. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.25869319.v2 (2025).","DOI":"10.6084\/m9.figshare.25869319.v2"},{"key":"9065_CR155","unstructured":"CannabisPangenomeShared. GitHub https:\/\/github.com\/anthony-aylward\/CannabisPangenomeShared (2024)."},{"key":"9065_CR156","unstructured":"CannabisPangenomeAnalyses. GitHub https:\/\/github.com\/padgittl\/CannabisPangenomeAnalyses (2024)."},{"key":"9065_CR157","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkac209","volume":"13","author":"P Woods","year":"2022","unstructured":"Woods, P., Price, N., Matthews, P. & McKay, J. K. Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa. G3 13, jkac209 (2022).","journal-title":"G3"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-09065-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-09065-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-09065-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,6]],"date-time":"2025-09-06T18:23:57Z","timestamp":1757183037000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-025-09065-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,28]]},"references-count":158,"journal-issue":{"issue":"8073","published-print":{"date-parts":[[2025,7,24]]}},"alternative-id":["9065"],"URL":"https:\/\/doi.org\/10.1038\/s41586-025-09065-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.05.21.595196","asserted-by":"object"},{"id-type":"doi","id":"10.21203\/rs.3.rs-4456891\/v1","asserted-by":"object"}]},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,28]]},"assertion":[{"value":"21 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 April 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 May 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"S.C. was a co-founder of Oregon CBD. A.R.G. and A.T. were employees of Oregon CBD. R.C.L. is a stakeholder in Saint Vrain Research LLC, which manufactures hemp-based products. T.P.M. is a founder of the carbon sequestration company CQuesta. A.H. is a co-founder of the genotyping company Veil Genomics. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}