Sun Jie, Wang Xiangfeng, Wang Ke, Meng Dian, Mu Yu, Zhang Lili, Wang Jingxuan, Yao Gang, Guo Li
Shandong Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
Nat Commun. 2025 Jul 1;16(1):5617. doi: 10.1038/s41467-025-61289-w.
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.
百合是具有巨大基因组的流行观赏和药用植物。由于组装复杂的千兆基因组面临挑战，我们对百合等大基因组植物的遗传结构、表观遗传调控和进化的了解仍然有限。在这里，我们利用PacBio HiFi和Hi-C测序数据，报告了许多现代百合品种的亲本王百合（Lilium regale）的高质量染色体水平的35.6 Gb参考基因组。我们表明，王百合的基因组扩展主要是由转座元件的广泛增殖导致长基因间区域和内含子区域，以及全基因组重复和串联重复引起的。王百合基因组富含重复序列（80.06%），编码大量长内含子的大基因（>10 Kb），这些内含子占所编码的67,862个基因长度的约90%。系统发育基因组学揭示了与防御反应和萜类生物合成相关的显著基因家族扩展，反映了其适应策略。通过多组学分析，我们揭示了转座元件活性和表观遗传调控如何影响转录、可变剪接和三维组织，这有助于其适应性进化。总的来说，这一显著改进的百合基因组组装和注释将成为百合遗传学、育种、保护生物学和被子植物基因组进化研究的重要资源。
