Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale)

Jie Sun, Xiangfeng Wang, Ke Wang, Dian Meng, Yu Mu, Lili Zhang, Jingxuan Wang, Gang Yao and Li Guo ()
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Jie Sun: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Xiangfeng Wang: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Ke Wang: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Dian Meng: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Yu Mu: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Lili Zhang: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Jingxuan Wang: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Gang Yao: Shandong Laboratory of Advanced Agricultural Sciences at Weifang
Li Guo: Shandong Laboratory of Advanced Agricultural Sciences at Weifang

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Lilies are popular ornamental and medicinal plants with gigantic genomes. Due to the challenge of assembling complex giga-genomes, our understanding of the genetic architecture, epigenetic regulation and evolution of large-genome plants such as lily remains limited. Here, we report a high-quality chromosome-level 35.6 Gb reference genome of royal lily (Lilium regale), a parent of many modern lily cultivars, using PacBio HiFi and Hi-C sequencing data. We show that genome expansion of L. regale is mainly caused by extensive proliferation of transposable elements resulting in long intergenic and intronic regions, along with whole-genome duplications and tandem repeats. L. regale genome is repeat-rich (80.06%) encoding abundant large genes (>10 Kb) with long introns that account for ~90% length of 67,862 genes encoded. Phylogenomics reveals significant gene family expansion related to defense response and biosynthesis of terpenoids, reflecting its adaptation strategy. Through multiomic analysis, we reveal how transposable element activity and epigenetic regulations may impact transcription, alternative splicing, and three-dimensional organization, which contribute to its adaptive evolution. Collectively, this significantly improved lily genome assembly and annotation will serve as an essential resource for research on lily genetics, breeding, conservation biology, and angiosperm genome evolution.

Date: 2025
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DOI: 10.1038/s41467-025-61289-w

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