New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences

Area of Science:

• Botany
• Plant Taxonomy
• Molecular Phylogenetics

Background:

• The genus *Lilium* (lilies) is globally significant, with Comber's classification widely used but with unresolved phylogenetic relationships.
• Previous molecular studies have not fully resolved the evolutionary history and sectional relationships within the *Lilium* genus.

Purpose of the Study:

• To construct a robust species tree for the genus *Lilium* using plastome data.
• To verify Comber's traditional classification system against molecular phylogenetic evidence.
• To identify reliable molecular markers within the *Lilium* plastome for future phylogenetic studies.

Main Methods:

• Phylogenetic analysis of 28 *Lilium* species plastomes.
• Construction of a species tree utilizing whole plastome sequences.
• Evaluation of specific genetic loci (*ycf1*, *trnF-ndhJ*, *trnT-psbD*) as phylogenetic markers.

Main Results:

• The genus *Lilium* was resolved into two primary lineages: Group A (East Asia + Europe) and Group B (Hengduan Mountains + North America).
• Comber's classification was partially supported, with evidence of polyphyly in sections *Pseudolirium* and *Leucolirion*, and *Martagon* diverging from *Sinomartagon*.
• The genetic regions *ycf1*, *trnF-ndhJ*, and *trnT-psbD* demonstrated high coincidence with the species tree, indicating their utility as molecular markers.

Conclusions:

• The study provides a refined phylogenetic framework for the genus *Lilium*, clarifying sectional relationships and biogeographical patterns.
• The identified molecular markers offer valuable tools for future research on lily evolution and diversification.
• Findings contribute to understanding the long-distance dispersal events shaping the genus *Lilium*'s distribution.