Lilium (lily) — celebrated for elegant silhouettes, intoxicating fragrance and symbolic purity — comprises ~120 wild species distributed across the north-temperate zone. Centuries of hybridisation have yielded the famed Oriental and Asiatic cultivars that dominate global cut-flower and garden markets. Among them, Lilium regale — native to the Min River Valley of Sichuan, China — was christened the “Royal Lily” by early-20th-century plant hunter Ernest H. Wilson, who acclaimed it “king of lilies” and used its virus-resistant germplasm to rescue Europe’s lily industry from lily-mottle-virus devastation. Today, virtually all ornamental lily cultivars trace part of their pedigree to L. regale. Yet over-collection and habitat loss now threaten this Chinese endemic, making its genome an essential resource for conservation, breeding and exploitation of its medicinal/food value.

 

The lily genome, however, is colossal — 30–48 Gb (10–16× human, 70–120× rice) — and highly heterozygous, rendering assembly one of the greatest challenges in modern genomics. Draft genomes of Lanzhou lily (The Innovation 2024) and Luding lily (Nat. Commun. 2025) opened the genomic era for the genus, but these assemblies remain fragmented.

 

 

On 1 July 2025, a study led by Dr. Li Guo (Peking University Institute of Advanced Agricultural Sciences / Shandong Laboratory of Advanced Agriculture Sciences in Weifang) in Nature Communications presents the first chromosome-level, high-contiguity genome of L. regale (35.6 Gb; contig N50 = 32.22 Mb; QV = 63.80) — currently the highest-quality lily reference genome.

 

Genome assembly & evolutionary history

l Twelve chromosomes (2.02–4.30 Gb each) encode 78,147 protein-coding genes.

l Comparative analyses reveal two whole-genome duplication (WGD) events after divergence from monocot ancestors and extensive tandem duplications contributing to environmental adaptation.

l Expanded gene families include terpene synthesis, disease resistance and long-gene splicing factors—likely evolutionary adaptations to a mega-genome environment.

 

 

Drivers of genome gigantism

l 80 % of the assembly is repetitive; 72.3 % is long-terminal-repeat retrotransposons (LTRs), the primary drivers of expansion.

l Bursts of intact LTR insertions coincide with recombination hotspots, while H3K9me2-marked solo-LTRs reflect epigenetic silencing.

l Intron inflation (often >100 kb) is largely attributable to LTR insertions, underpinning the ultra-long genes characteristic of lilies.

 

 

Epigenomic regulation of genome function

l Full-length transcriptomics uncovered 2,580 alternative-splicing events; cassette-exon usage correlates with transposon density, CHG methylation and histone modifications, revealing a balance between splicing flexibility and transcript stability.

l Hi-C 3-D modelling uncovered extraordinary inter-chromosomal interactions and TAD-like structures; H3K9me2 is enriched at TAD boundaries, implicating transposons in higher-order chromatin organisation.

l Collectively, these mechanisms illustrate how L. regale maintains structural integrity and gene regulation within a 35.6 Gb nucleus.

 

 

This reference genome fills the last major gap for ultra-large plant genomes, accelerates functional genomics, precision breeding and conservation genomics of Lilium, and deepens our understanding of how transposons sculpt genome architecture and adaptive evolution.

 

Dr. Li Guo is the corresponding author. Research assistants Jie Sun and Xiangfeng Wang are co-first authors; MS student Ke Wang (Shandong Agricultural University joint graduate program) and research assistants Dian Meng, Yu Mu, Jingxuan Wang, Lili Zhang and Gang Yao provided critical technical support. Funding came from the Shandong Provincial Natural Science Foundation, Taishan Scholar Program and Shandong Key R&D Program, with computational resources provided by the High-Performance Computing Center of Peking University Institute of Advanced Agricultural Sciences.

 

Paper link: https://doi.org/10.1038/s41467-025-59336-7