The evolutionary tale of lilies: Giant genomes derived from transposon insertions and polyploidization

Lily (Lilium spp.), known as the "king of bulbous flowers," has high ornamental and medicinal value due to its attractive, fragrant flowers and nutritious bulbs. The Lilium genus comprises approximately 115 perennial bulbous herbal species distributed in the Northern hemisphere, including 55 species and 18 varieties that were discovered in China. The rich diversity of lilies in China likely contributes to their extensive utilization and provides valuable resources for scientific studies. However, their giant genomes pose a challenge to high-quality genome assembly, and there is no reference genome for this lineage. To date, only a few giant genomes have been published due to technical difficulties and high costs.1 The substantial diversity in genome size among organisms is of fundamental biological significance. However, the correlation between organismal complexity and genome size remains tenuous.2 Sequencing and assembling large/complex genomes remain challenging due to issues such as polyploidy, high heterozygosity, and high repeat ratios. Because they have significantly larger genomes than other eukaryotes, almost all Lilium species could serve as ideal models in which to study the relationship between organismal complexity and genome size. L. davidii var. unicolor, the only edible sweet lily variety, has been cultivated for ∼150 years in Lanzhou, China, providing an important source of income for local farmers. We selected this variety for genome sequencing to acquire valuable data for studying the giant genomes of lilies and, thereby, facilitate their genetic improvement and enhance breeding efforts.