ArticleNature communications2025
Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Genome-wide analysis of the HSF gene family in lily and functional characterization of LdHSFC1 under heat stress.Plant cell reports · 2026Article
- Sarcandra glabra genome unveils functional conservation and divergence of O-methyltransferases catalyzing isofraxidin biosynthesis in angiosperms.Nature communications · 2026Article
- Haplotype-resolved autotetraploid genome of Dioscorea nipponica provides insights into recent polyploidization, metabolic rewiring, and environmental adaptation.The Plant journal : for cell and molecular biology · 2026Article
- Genome-Wide Identification of thePlants (Basel, Switzerland) · 2026Article
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- A near-complete genome assembly of onion resolves its genomic architecture, origin, and evolution.Plant communications · 2026Article
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- The Nigella damascena genome provides insights into transposable element-driven genomic gigantism and trait evolution.Nature communications · 2026Article
- Genome-wide identification and expression analysis of the bHLH gene family in Lilium davidii var. unicolor and its response to abiotic stress.BMC plant biology · 2026Article
- Genome-Wide Analysis of the MADS-Box Gene Family and Expression Pattern Under Abiotic Stresses inInternational journal of molecular sciences · 2026Article
- A comprehensive review of physiological and molecular responses to stress of lilies (genusHorticulture research · 2026Article
- LGD: a comprehensive online database of Liliales based on multi-omics data.Horticulture research · 2026Article
- A new efficient immunoprotocol to detect chromosomal/nuclear proteins along with repetitive DNA in squash preparations of formalin-fixed, long-stored root tips.Plant methods · 2025Article
- Genome-Wide Identification and Expressional Analysis of theInternational journal of molecular sciences · 2025Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
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9 authors.
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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.
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