Integrative multi-omics analysis reveals the genetic architecture of floral traits in Anthurium

Abstract

Anthurium, a highly diverse genus in the family Araceae, is well known for its ornamental spathes and spadices. However, limited genomic resources hinder the study of floral traits and their evolutionary histories. Here, we present high-quality chromosome-level genome assemblies of Anthurium andraeanum and Anthurium scherzerianum. Comparative genomics revealed extensive chromosomal rearrangements and species-specific transposon expansions, which likely contributed to genome divergence. Two lineage-specific whole-genome duplications were identified, associated with gene family expansions linked to stress adaptation. Population structure analysis uncovered strong genetic admixture, reflecting widespread historical hybridization. Integrated transcriptomic and metabolomic analyses revealed dynamic regulatory networks governing spathe coloration through flavonoid-anthocyanin pathways. In addition, CER3, KCS1, and KCS3 were identified as key regulators involved in wax biosynthesis. Notably, inflorescence evolution correlates with the loss of the floral identity genes SOC1 and AGL6, highlighting conserved developmental pathways and lineage-specific innovations. Our findings provide foundational genomic resources for understanding Anthurium evolution, offer molecular targets for breeding programs, and elucidate transposon-driven genome expansion mechanisms that advance our knowledge of speciation in tropical epiphytes with exceptionally large genomes.

Acknowledgements

This project was supported by the Project of National Key Laboratory for Tropical Crop Breeding (NKLTCB-ZX04), the Central Public-interest Scientific Institution Basal Research Fund (1630032023014; 1630032024024), the Hainan Major Science and Technology Program (ZDKJ2021015), the Scientific Research Foundation for Principle Investigator, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-QD2022004), the Funding of Major Scientific Research Tasks, Kunpeng Institute of Modern Agriculture at Foshan (KIMA-ZDKY2022004), the Chinese Academy of Agricultural Sciences Elite Youth Program (grant 110243160001007), the Taizhou Seed Industry Research and Development Project (2024-06), and Hainan Provincial Natural Science Foundation of China (325RC822).

Authors contributions

Z.W., J.N., D.T., and J.Y. conceived and supervised the project, acquired funding, provided resources, and contributed to project administration, methodology, and validation. S.L. and C.S. curated data, conducted the investigation, and wrote the original draft. D.P., Y.W., X.Z., Y.Y., M.J., Q.L., S.X., X.L., H.L., J.L., C.Z., X.W., J.S., and L.R.T. contributed to writing—review and editing. S.L., C.S., D.P., and Y.W. were responsible for visualization and formal analysis. All authors read and approved the final manuscript.

Data availability

All data supporting the results of this study are included in the manuscript and its additional files. All sequencing reads, including Illumina, PacBio HiFi, Hi-C, RNA-seq, and the assembly and annotation files have been deposited in the China National GeneBank (https://www.cngb.org/) under project number CNP0006988.

Conflicts of interest statement

The authors declare no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

References

[1] Carlsen M, Croat T. A molecular phylogeny of the species-rich neotropical genus Anthurium (Araceae) based on combined chloroplast and nuclear DNA. Syst Bot. 2013; 38:576-88

[2] Carlsen MM, Croat TB. An analysis of the sectional classifica-tion of Anthurium (Araceae): comparing infrageneric group-ings and their diagnostic morphology with a molecular phy-logeny of the genus. Ann Mo Bot Gard. 2019; 104:69-82

[3] Croat TB, Ortiz OO. Distribution of Araceae and the diversity of life forms. Acta Soc Bot Pol. 2020; 89:8939

[4] Reimuth J, Zotz G. The biogeography of the megadiverse genus Anthurium (Araceae). Bot J Linn Soc. 2020; 194:164-76

[5] Croat TB. A Revision of the Genus Anthurium (Araceae) of Mexico and Central America. Part II: Panama. Monographs in sustematic botany from the missouri botamical garden. St. Louis, MO, USA: Missouri Botanical Garden Press; 1986: 157-232

[6] Croat TB. Ecology and life forms of Araceae. Aroideana. 1988; 11:4-55

[7] Croat TB, Carlsen MM. A reassessment of Anthurium species with palmately divided leaves, and a reinterpretation of Anthurium section Dactylophyllium (Araceae). PhytoKeys. 2013; 23:41-54

[8] Croat T, Grib J, Ortiz O. et al. The current status of Anthurium sect. Porphyrochitonium (Araceae) and allies, with many new species from central and South America. J Int Aroid Soc. 2022; 45:48-436

[9] de Castro Camelo M, Temponi LG, Coelho MAN. et al. Fruit morphology in Anthurium sect. Pachyneurium from Brazil (Araceae) and its taxonomic implications. Flora. 2023; 309:152406

[10] Tay J, Werner J, Zotz G. Morphological diversity of the vela-men radicum in the genus Anthurium (Araceae). Plant Biol. 2024; 26:679-90

[11] Elibox W, Umaharan P. Genetic basis for productivity in Anthurium andraeanum Hort. HortScience. 2014; 49:859-63

[12] Fitch MMM, Leong TCW, He X. et al. Improved transformation of Anthurium. HortScience. 2011; 46:358-64

[13] Islam M, Mehraj H, Roni M. et al. Varietal study of Anthurium (Anthurium andraeanum) as a cut flower in Bangladesh. J Bangladesh Acad Sci. 2013; 37:103-7

[14] Li C, Qiu J, Huang S. et al. AaMYB3 interacts with AabHLH1 to regulate proanthocyanidin accumulation in Anthurium andraeanum (Hort.) —another strategy to modulate pigmen-tation. Hortic Res. 2019; 6:1-16

[15] Iwata RY. Anthocyanins and Other Flavonoids in Anthurium Andraeanum Linden ex Andre. Dissertation. Honolulu, HI, USA: University of Hawai’i at Manoa; 1980.

[16] Jayaprada N, Fukai S, Geekiyanage S. Does an R2R3-MYB transcription factor affect Anthurium spathe colour variation via regulation of vacuolar pH? J Natl Sci Found Sri Lanka. 2023; 51:629-41

[17] Li CH, Yang GS, Huang SR. et al. Characterisation of flavonoids in Anthurium spathes and their contribution to spathe colouration. J Hortic Sci Biotechnol. 2013; 88:208-15

[18] Toves PJ. Anthurium Flower Color:Histology and Genetic Manipulation. Dissertation. Honolulu, HI, USA: University of Hawai’i at Manoa; 2022

[19] Cheng G, Wang L, Wu H. et al. Variation in petal and leaf wax deposition affects cuticular transpiration in cut lily flowers. Front Plant Sci. 2021; 12:781987

[20] Peng Z, Chen H, Niu B. et al. Composition and micromor-phological determination of blue honeysuckle fruit (Lonicera caerulea L.) cuticular wax and its effects on fruit post-harvest quality. Food Chem. 2025; 463:141330

[21] Powar V, Bhargava B, Vikas G. Study on waxing of cut foliage post harvest life of few ornamental species. J Appl Nat Sci. 2014; 6:619-24

[22] Kim H, Yu S, Jung SH. et al. The F-box protein SAGL1 and ECERIFERUM3 regulate cuticular wax biosynthesis in response to changes in humidity in Arabidopsis. Plant Cell. 2019; 31:2223-40

[23] Lewandowska M, Keyl A, Feussner I. Wax biosynthesis in response to danger: its regulation upon abiotic and biotic stress. New Phytol. 2020; 227:698-713

[24] Li S, Zhang X, Huang H. et al. Deciphering the core shunt mechanism in Arabidopsis cuticular wax biosynthesis and its role in plant environmental adaptation. Nat Plants. 2025; 11:165-75

[25] Riederer M, Schreiber L. Protecting against water loss: anal-ysis of the barrier properties of plant cuticles. J Exp Bot. 2001; 52:2023-32

[26] Elibox W, Umaharan P. A study of morphophysiologi-cal descriptors of cultivated Anthurium andraeanum Hort. HortScience. 2012; 47:1234-40

[27] Barabe D, Lacroix C. Developmental morphology of the flower of Anthurium jenmanii: a new element in our under-standing of basal Araceae. Botany. 2008; 86:45-52

[28] Buzgo M. Flower structure and development of Araceae compared with alismatids and Acoraceae. Bot J Linn Soc. 2001; 136:393-425

[29] Theißen G Development of floral organ identity: stories from the MADS house. Current Opinion in Plant Biology. 2001; 4:75-85

[30] Becker A, Theißen G. The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Molecular Phylogenetics and Evolution. 2003; 29:464-89

[31] Chouteau M, Gibernau M, BarabE D. Relationships between floral characters, pollination mechanisms, life forms, and habitats in Araceae. Bot J Linn Soc. 2008; 156:29-42

[32] Liu D, Wang Q, Yang C. et al. Flower diversity and pollination strategy in Araceae. Biodivers Sci. 2022; 30:21426

[33] Zhu G, Wang S, Huang Z. et al. Rewiring of the fruit metabolome in tomato breeding. Cell. 2018; 172:249-261.e12

[34] Song C, Tian J, Xie D. et al. Metabolomic and transcrip-tomic analyses provide insight into the variation of floral scent and molecular regulation in different cultivars and flower development of Curcuma alismatifolia. Hortic Res. 2025;12:uhae348

[35] Wan S, Schaap PJ, Suarez-Diez M. et al. Omics strategies for plant natural product biosynthesis. Genomics Commun. 2025; 2:e011

[36] Chen D, Yang T, Chen H. et al. Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana. Plant Biotech-nol J. 2025; 23:4109-25

[37] Lei P, Pan M, Kang S. et al. A premature termination codon mutation in the onion AcCER2 gene is associated with both glossy leaves and thrip resistance. Hortic Res. 2025;12:uhaf006

[38] Zhou L, Wu S, Chen Y. et al. Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms. Nat Commun. 2024; 15:8469

[39] Zhang X, Lin S, Peng D. et al. Integrated multi-omic data and analyses reveal the pathways underlying key orna-mental traits in carnation flowers. Plant Biotechnol J. 2022; 20:1182-96

[40] Zhang X, Wu Q, Lan L. et al. Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits. Mol Hor-tic. 2024; 4:14

[41] Collins FS, Green ED, Guttmacher AE. et al. A vision for the future of genomics research. Nature. 2003; 422:835-47

[42] Koonin EV, Aravind L, Kondrashov AS. The impact of com-parative genomics on our understanding of evolution. Cell. 2000; 101:573-6

[43] Liu Y-Y, Yu C-L, Liu Y-J. et al. An autotetraploid genome of Corydalis sheareri provides insight into the evolution and benzylisoquinoline alkaloids diversity of Corydalis. Genomics Commun. 2025; 2:e002

[44] Wang C, Han B. Twenty years of rice genomics research: from sequencing and functional genomics to quantitative genomics. Mol Plant. 2022; 15:593-619

[45] Yang Y, Du W, Li Y. et al. Recent advances and challenges in de novo genome assembly. Genomics Commun. 2025; 2: e014

[46] Cusimano N, Bogner J, Mayo SJ. et al. Relationships within the Araceae: comparison of morphological patterns with molecular phylogenies. Am J Bot. 2011; 98:654-68

[47] Haigh AL, Gibernau M, Maurin O. et al. Target sequence data shed new light on the infrafamilial classification of Araceae. Am J Bot. 2023; 110:e16117

[48] Henriquez CL, Arias T, Pires JC. et al. Phylogenomics of the plant family Araceae. Mol Phylogenet Evol. 2014; 75:91-102

[49] Nauheimer L, Metzler D, Renner SS. Global history of the ancient monocot family Araceae inferred with mod-els accounting for past continental positions and previous ranges based on fossils. New Phytol. 2012; 195:938-50

[50] Zhao L, Yang Y-Y, Qu X-J. et al. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the his-tory of diversification and adaptations in the Araceae. Ann Bot. 2023; 131:199-214

[51] Lyu H, Sim SB, Geib SM. et al. Chromosome-level genome assembly and annotation of Anthurium amnicola. Sci Data. 2025; 12:605

[52] Jiao Y. Double the genome, double the fun: genome duplica-tions in angiosperms. Mol Plant. 2018; 11:357-8

[53] Ren R, Wang H, Guo C. et al. Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol Plant. 2018; 11:414-28

[54] Sun P, Jiao B, Yang Y. et al. WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol Plant. 2021; 15:1841-51

[55] Shi T, Huneau C, Zhang Y. et al. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evo-lution. Nat Plants. 2022; 8:764-77

[56] Gao Y, Zhang Y, Feng C. et al. A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis. Comput Struct Biotech-nol J. 2022; 20:1002-11

[57] Qian Z, Li Y, Yang J. et al. The chromosome-level genome of a free-floating aquatic weed Pistia stratiotes provides insights into its rapid invasion. Mol Ecol Resour. 2022; 22:2732-43

[58] Qian Z, Ding J, Li Z. et al. The high-quality Pinellia pedati-secta genome reveals a key role of tandem duplication in the expansion of its agglutinin genes. Hortic Res. 2023;10: uhac289

[59] Wang W, Haberer G, Gundlach H. et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun. 2014; 5:3311

[60] Yin J, Jiang L, Wang L. et al. A high-quality genome of taro (Colocasia esculenta (L.) Schott), one of the world’s oldest crops. Mol Ecol Resour. 2021; 21:68-77

[61] Livingstone K, Rieseberg L. Chromosomal evolution and speciation: a recombination-based approach. New Phytol. 2004; 161:107-12

[62] Rieseberg LH. Chromosomal rearrangements and specia-tion. Trends Ecol Evol. 2001; 16:351-8

[63] Sajeevan RS. Cuticular waxes and its application in crop improvement. In: Harohalli Masthigowda M, Gopalareddy K, Khobra R, Singh G, Pratap Singh G,editors. Translating Phys-iological Tools to Augment Crop Breeding. Springer Nature Singapore: Singapore, 2023,147-76

[64] Zhang ZH, Gozdzik J, Jetter R. Characterization of the closely related Arabidopsis thaliana β-ketoacyl-CoA syn-thases KCS3, KCS12 and KCS19. Plant J. 2024; 119:490-507

[65] Zhang Y, Qin G, Tsuge T. et al. Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis. Plant Cell. 2008; 20:1538-54

[66] Li W, Tian Z, Yu D. WRKY 13 acts in stem development in Arabidopsis thaliana. Plant Sci. 2015; 236:205-13

[67] Caselli F, Ferrario C, Beretta VM. et al. Behind phyllotaxis, within the meristem: a REM-ARF complex shapes inflores-cence in Arabidopsis thaliana. Plant J. 2025; 121:e70041

[68] Li Y, Peng L, Wang X. et al. Reduction in chloroplastic ribulose-5-phosphate-3-epimerase decreases photosynthetic capacity in Arabidopsis. Front Plant Sci. 2022; 13:813241

[69] Gao Y, Yuan G, Niu C. et al. Genetic diversity and popu-lation structure of the dvel’s tongue arum (Amorphophal-lus konjac) in South-Western China. Pak J Bot. 2018; 50: 999-1004

[70] Kreike C, Van Eck H, Lebot V. Genetic diversity of taro, Colo-casia esculenta (L.) Schott, in Southeast Asia and the Pacific. Theor Appl Genet. 2004; 109:761-8

[71] Tang R, Liu E, Zhang Y. et al. Genetic diversity and popu-lation structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River. BMC Genet. 2020; 21:102

[72] Ho EK, Bartkowska M, Wright SI. et al. Population genomics of the facultatively asexual duckweed Spirodela polyrhiza. New Phytol. 2019; 224:1361-71

[73] Becker A, Theißen G. The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol. 2003; 29:464-89

[74] Coen ES, Meyerowitz EM. The war of the whorls: genetic interactions controlling flower development. Nature. 1991; 353:31-7

[75] Böhlenius H, Huang T, Charbonnel-Campaa L. et al. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science. 2006; 312: 1040-3

[76] Lee J, Lee I. Regulation and function of SOC1, a flowering pathway integrator. J Exp Bot. 2010; 61:2247-54

[77] Dreni L, Zhang D. Flower development: the evolutionary his-tory and functions of the AGL6 subfamily MADS-box genes. J Exp Bot. 2016; 67:1625-38

[78] Sapir Y, Gallagher MK, Senden E. What maintains flower colour variation within populations? Trends Ecol Evol. 2021; 36:507-19

[79] Li J, Tan Q, Yi M. et al. Identification of key genes respon-sible for green and white colored spathes in Anthurium andraeanum (Hort.). Front Plant Sci. 2023; 14:1208226

[80] Osorio-Guarín JA, Gopaulchan D, Quanckenbush C. et al. Comparative transcriptomic analysis reveals key compo-nents controlling spathe color in Anthurium andraeanum ( hort.). PLoS One. 2021; 16:e0261364

[81] Zhang MF, Wang JQ, Liu RL. et al. CsMYB96 confers resistance to water loss in citrus fruit by simultaneous regulation of water transport and wax biosynthesis. J Exp Bot. 2022; 73: 953-66

[82] Kong LY, Liu YN, Zhi PF. et al. Origins and evolution of cuticle biosynthetic machinery in land plants. Plant Physiol. 2020; 184:1998-2010

[83] Lee SB, Suh MC. Regulatory mechanisms underlying cuticu-lar wax biosynthesis. J Exp Bot. 2022; 73:2799-816

[84] Lu HC, Lam SH, Zhang DY. et al. R2R3-MYB genes coordinate conical cell development and cuticular wax biosynthesis in Phalaenopsis aphrodite. Plant Physiol. 2022; 188:318-31

[85] Zhang YL, Tian Y, Man YY. et al. Apple SUMO E3 ligase MdSIZ1 regulates cuticular wax biosynthesis by SUMOylat-ing transcription factor MdMYB30. Plant Physiol. 2023; 191: 1771-88

[86] Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011; 27:764-70

[87] Sun H, Ding J, Piednoël M. et al. findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. Bioinformatics. 2018; 34:550-7

[88] Manni M, Berkeley MR, Seppey M. et al. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokary-otic, and viral genomes. Mol Biol Evol. 2021; 38:4647-54

[89] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25: 1754-60

[90] Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34:3094-100

[91] Marçais G, Delcher AL, Phillippy AM. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018; 14:e1005944

[92] Goel M, Sun H, Jiao W-B. et al. SyRI: finding genomic rear-rangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019; 20:1-13

[93] Danecek P, Bonfield JK, Liddle J. et al. Twelve years of SAM-tools and BCFtools. Gigascience. 2021;10:giab008

[94] Van der Auwera GA, O’Connor BD. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. Sebastopol, CA: O’Reilly Media; 2020

[95] Li T, Ma X, Li N. et al. Genome-wide association study discov-ered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J. 2017; 15: 1520-32

[96] Purcell S, Neale B, Todd-Brown K. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81:559-75

[97] Zhou H, Alexander D, Lange K. A quasi-Newton method for accelerating the convergence of iterative optimization algo-rithms. Stat Comput. 2009; 21:261-73

[98] Chen C, Wu Y, Li J. et al. TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining. Mol Plant. 2023; 16:1733-42

[99] Chen S, Zhou Y, Chen Y. et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884-90

[100] Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12:357-60

[101] Pertea M, Pertea GM, Antonescu CM. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33:290-5

[102] Pertea M, Kim D, Pertea GM. et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11:1650-67

[103] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15:1-21

[104] Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30:923-30

[105] Chang Y-M, Lin H-H, Liu W-Y. et al. Comparative transcrip-tomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proc Natl Acad Sci. 2019; 116:3091-9

[106] Mistry J, Chuguransky S, Williams L. et al. Pfam:the pro-tein families database in 2021. Nucleic Acids Res. 2020;49: D412-9

[107] Eddy S. HMMER User’s Guide. Department of Genetics, Wash-ington University School of Medicine; 1992:13

[108] Katoh K, Standley DM. MAFFT multiple sequence align-ment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30:772-80

[109] Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylo-genetic analyses. Bioinformatics. 2009; 25:1972-3

[110] Minh BQ, Schmidt HA, Chernomor O. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020; 37:1530-4

[111] Arora R, Agarwal P, Ray S. et al. MADS-box gene family in rice: genome-wide identification, organization and expres-sion profiling during reproductive development and stress. BMC Genomics. 2007; 8:242

[112] Ma X, Vanneste S, Chang J. et al. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environ-ment. Nat Plants. 2024; 10:240-55

[113] Parenicová L, De Folter S, Kieffer M. et al. Molecular and phylogenetic analyses of the complete MADS-box transcrip-tion factor family in Arabidopsis: new openings to the MADS world. Plant Cell. 2003; 15:1538-51

[114] Schilling S, Kennedy A, Pan S. et al. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplica-tions, functional conservation and putative neofunctional-ization. New Phytol. 2020; 225:511-29