1National Key Laboratory for Tropical Crop Breeding, Key Laboratory of Gene Resources and Germplasm Enhancement in Southern China, MARA, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China 2Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China 3Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China 4Chongqing Key Laboratory for Germplasm Innovation of Special Aromatic Spice Plants, College of Smart Agriculture, Chongqing University of Arts and Sciences, Chongqing 402160, China 5School of Ecology, Hainan University, Haikou 570228, China 6College of Horticulture, Shanxi Agricultural University, Taiyuan 030031, China 7Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Academy of Agricultural Sciences, Hangzhou, China 8Taizhou Suzhong Horticulture Co., Ltd., Taizhou, China 9Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80525, USA 10Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China 11The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China 12Shengnan Lin, Chao Song, Dan Peng and Yaru Wang contributed equally to this work *Corresponding author. E-mail: yinjunmei@catas.cn,tdqing@zaas.ac.cn,wuzhiqiang@caas.cn,niujunhai@catas.cn
Received: 23 May 2025 Revised: 15 Nov 2025 Published online: 08 Nov 2025
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.
, Danqing Tian7 ,
