[1]

The Angiosperm Phylogeny Group. 2016. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society 181:1−20

doi: 10.1111/boj.12385
[2]

Hao DC, Xu LJ, Zheng YW, Lyu HY, Xiao PG. 2022. Mining therapeutic efficacy from treasure chest of biodiversity and chemodiversity: pharmacophylogeny of ranunculales medicinal plants. Chinese Journal of Integrative Medicine 28:1111−1126

doi: 10.1007/s11655-022-3576-x
[3]

Bhambhani S, Kondhare KR, Giri AP. 2021. Diversity in chemical structures and biological properties of plant alkaloids. Molecules 26(11):3374

doi: 10.3390/molecules26113374
[4]

Tian Y, Kong L, Li Q, Wang Y, Wang Y, et al. 2024. Structural diversity, evolutionary origin, and metabolic engineering of plant specialized benzylisoquinoline alkaloids. Natural Product Reports 41:1787−1810

doi: 10.1039/D4NP00029C
[5]

Minami H, Dubouzet E, Iwasa K, Sato F. 2007. Functional analysis of norcoclaurine synthase in Coptis japonica. The Journal of Biological Chemistry 282:6274−6282

doi: 10.1074/jbc.M608933200
[6]

Morishige T, Tamakoshi M, Takemura T, Sato F. 2010. Molecular characterization of O-methyltransferases involved in isoquinoline alkaloid biosynthesis in Coptis japonica. Proceedings of the Japan Academy, Series B, Physical and Biological Sciences 86:757−768

doi: 10.2183/pjab.86.757
[7]

Guo L, Winzer T, Yang X, Li Y, Ning Z, et al. 2018. The opium poppy genome and morphinan production. Science 362:343−347

doi: 10.1126/science.aat4096
[8]

Hong UVT, Tamiru-Oli M, Hurgobin B, Lewsey MG. 2025. Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy. Journal of Experimental Botany 76:35−51

doi: 10.1093/jxb/erae317
[9]

Menéndez-Perdomo IM, Facchini PJ. 2023. Elucidation of the (R)-enantiospecific benzylisoquinoline alkaloid biosynthetic pathways in sacred lotus (Nelumbo nucifera). Scientific Reports 13:2955

doi: 10.1038/s41598-023-29415-0
[10]

Lee EJ, Facchini P. 2010. Norcoclaurine synthase is a member of the pathogenesis-related 10/bet v1 protein family. The Plant Cell 22:3489−3503

doi: 10.1105/tpc.110.077958
[11]

Ziegler J, Facchini PJ. 2008. Alkaloid biosynthesis: metabolism and trafficking. Annual Review of Plant Biology 59:735−769

doi: 10.1146/annurev.arplant.59.032607.092730
[12]

Hu Y, Wang J, Liu L, Yi X, Wang X, et al. 2025. Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis. Nature Communications 16:4039

doi: 10.1038/s41467-025-59343-8
[13]

Shen G, Luo Y, Yao Y, Meng G, Zhang Y, et al. 2022. The discovery of a key prenyltransferase gene assisted by a chromosome-level Epimedium pubescens genome. Frontiers in Plant Science 13:1034943

doi: 10.3389/fpls.2022.1034943
[14]

Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890

doi: 10.1093/bioinformatics/bty560
[15]

Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150−3152

doi: 10.1093/bioinformatics/bts565
[16]

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389−3402

doi: 10.1093/nar/25.17.3389
[17]

Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, et al. 2016. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant 9:1667−1670

doi: 10.1016/j.molp.2016.09.014
[18]

Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583−2585

doi: 10.1093/bioinformatics/btx198
[19]

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8:1494−1512

doi: 10.1038/nprot.2013.084
[20]

Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. 2019. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Research 47:W5−W10

doi: 10.1093/nar/gkz342
[21]

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972−1973

doi: 10.1093/bioinformatics/btp348
[22]

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−274

doi: 10.1093/molbev/msu300
[23]

Zhang C, Rabiee M, Sayyari E, Mirarab S. 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19:153

doi: 10.1186/s12859-018-2129-y
[24]

Kumar S, Suleski M, Craig JM, Kasprowicz AE, Sanderford M, et al. 2022. TimeTree 5: an expanded resource for species divergence times. Molecular Biology and Evolution 39(8):msac174

doi: 10.1093/molbev/msac174
[25]

Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301−302

doi: 10.1093/bioinformatics/19.2.301
[26]

Chen H, Zwaenepoel A, Van de Peer Y. 2024. wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinformatics 40(5):btae272

doi: 10.1093/bioinformatics/btae272
[27]

Van Dongen S. 2008. Graph clustering via a discrete uncoupling process. SIAM Journal on Matrix Analysis and Applications 30:121−141

doi: 10.1137/040608635
[28]

Price MN, Dehal PS, Arkin AP. 2010. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490

doi: 10.1371/journal.pone.0009490
[29]

Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238

doi: 10.1186/s13059-019-1832-y
[30]

Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, et al. 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research 48:D265−D268

doi: 10.1093/nar/gkz991
[31]

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research 37:W202−W208

doi: 10.1093/nar/gkp335
[32]

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, et al. 2020. HyPhy 2.5-a customizable platform for evolutionary hypothesis testing using phylogenies. Molecular Biology and Evolution 37:295−299

doi: 10.1093/molbev/msz197
[33]

Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, et al. 2018. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research 46:W296−W303

doi: 10.1093/nar/gky427
[34]

Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, et al. 2021. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Science 30:70−82

doi: 10.1002/pro.3943
[35]

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210−3212

doi: 10.1093/bioinformatics/btv351
[36]

Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473:97−100

doi: 10.1038/nature09916
[37]

Wu S, Han B, Jiao Y. 2020. Genetic contribution of paleopolyploidy to adaptive evolution in angiosperms. Molecular Plant 13:59−71

doi: 10.1016/j.molp.2019.10.012
[38]

Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, et al. 2018. Impact of whole-genome duplication events on diversification rates in angiosperms. American Journal of Botany 105:348−363

doi: 10.1002/ajb2.1060
[39]

Becker A, Bachelier JB, Carrive L, Conde E Silva N, Damerval C, et al. 2024. A cornucopia of diversity-Ranunculales as a model lineage. Journal of Experimental Botany 75:1800−1822

doi: 10.1093/jxb/erad492
[40]

Liu X, Bu J, Ma Y, Chen Y, Li Q, et al. 2021. Functional characterization of (S)-N-methylcoclaurine 3'-hydroxylase (NMCH) involved in the biosynthesis of benzylisoquinoline alkaloids in Corydalis yanhusuo. Plant Physiology and Biochemistry 168:507−515

doi: 10.1016/j.plaphy.2021.09.042
[41]

Morris JS, Yu L, Facchini PJ. 2020. A single residue determines substrate preference in benzylisoquinoline alkaloid N-methyltransferases. Phytochemistry 170:112193

doi: 10.1016/j.phytochem.2019.112193
[42]

Li K, Chen X, Zhang J, Wang C, Xu Q, et al. 2022. Transcriptome analysis of Stephania tetrandra and characterization of norcoclaurine-6-O-methyltransferase involved in benzylisoquinoline alkaloid biosynthesis. Frontiers in Plant Science 13:874583

doi: 10.3389/fpls.2022.874583
[43]

Hagel JM, Morris JS, Lee EJ, Desgagné-Penix I, Bross CD, et al. 2015. Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC Plant Biology 15:227

doi: 10.1186/s12870-015-0596-0
[44]

Leebens-Mack JH, Barker MS, Carpenter EJ, Deyholos MK, Gitzendanner MA, et al. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574:679−685

doi: 10.1038/s41586-019-1693-2
[45]

Wang W, Lu AM, Ren Y, Endress ME, Chen ZD. 2009. Phylogeny and classification of Ranunculales: evidence from four molecular loci and morphological data. Perspectives in Plant Ecology, Evolution and Systematics 11:81−110

doi: 10.1016/j.ppees.2009.01.001
[46]

Kim S, Soltis DE, Soltis PS, Zanis MJ, Suh Y. 2004. Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody? Molecular Phylogenetics and Evolution 31:16−30

doi: 10.1016/j.ympev.2003.07.017
[47]

Sun Y, Moore MJ, Lin N, Adelalu KF, Meng A, et al. 2017. Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family. BMC Genomics 18:592

doi: 10.1186/s12864-017-3956-3
[48]

Torsvik TH, Cocks LRM. 2016. Earth history and palaeogeography. Cambridge: Cambridge University Press
[49]

He J, Lyu R, Luo Y, Xiao J, Xie L, et al. 2022. A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae. Molecular Phylogenetics and Evolution 174:107545

doi: 10.1016/j.ympev.2022.107545
[50]

Linnert C, Robinson SA, Lees JA, Bown PR, Pérez-Rodríguez I, et al. 2014. Evidence for global cooling in the Late Cretaceous. Nature Communications 5:4194

doi: 10.1038/ncomms5194
[51]

Westerhold T, Marwan N, Drury AJ, Liebrand D, Agnini C, et al. 2020. An astronomically dated record of Earth's climate and its predictability over the last 66 million years. Science 369:1383−1387

doi: 10.1126/science.aba6853
[52]

Favre A, Päckert M, Pauls SU, Jähnig SC, Uhl D, et al. 2015. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas. Biological Reviews 90:236−253

doi: 10.1111/brv.12107
[53]

Hewitt GM. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58:247−276

doi: 10.1006/bijl.1996.0035
[54]

Liu Y, Wang B, Shu S, Li Z, Song C, et al. 2021. Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids. Nature Communications 12:3276

doi: 10.1038/s41467-021-23611-0
[55]

Yang X, Gao S, Guo L, Wang B, Jia Y, et al. 2021. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nature Communications 12:6030

doi: 10.1038/s41467-021-26330-8
[56]

Weng JK, Philippe RN, Noel JP. 2012. The rise of chemodiversity in plants. Science 336:1667−1670

doi: 10.1126/science.1217411
[57]

Firn RD, Jones CG. 2000. The evolution of secondary metabolism - a unifying model. Molecular Microbiology 37:989−994

doi: 10.1046/j.1365-2958.2000.02098.x