Integrating morphological data and chloroplast genome analyses provides novel insights into the phylogeny of Lilium species in China

Background: The genus Lilium comprises plants with combined ornamental, edible, and medicinal values, distributed primarily in the temperate regions of the Northern Hemisphere, subtropical mountainous areas, Southeast Asia, and tropical zones. Although previous studies using various molecular markers have provided significant insights into species delimitation and phylogeography of Lilium , the taxonomic status of some species within this genus remains unresolved, necessitating further detailed investigation. Results: The chloroplast genomes (cpDNAs) of Lilium species range in size from 151,655 to 153,235 bp and exhibit a typical quadripartite structure, comprising a large single-copy region (LSC, 81,222–82,496 bp), a small single-copy region (SSC, 17,031–17,792 bp), and two inverted repeat regions (IRs, 26,271–26,990 bp). Twelve highly variable regions were identified: matK-trnK, trnS-trnG, rps16, trnE-trnT-psbD, trnT-trnL, trnF-ndhJ, trnP-psaJ-rpl33, psbE-petL, petD-rpoA, rpl32-trnL, ndhD, and rps15-ycf1. These findings suggest that combining morphological data with complete chloroplast genome sequences is more effective for resolving phylogenetic relationships among Lilium species. This study not only advances our understanding of plant diversity within the genus Lilium but also provides a critical theoretical foundation and empirical data to support taxonomic research and conservation strategies for these species. Conclusion: In this study, we analyzed the complete chloroplast genomes of 63 Lilium species and proposed a new species, Lilium jiulongense , clarified its phylogenetic placement. Additionally, this work provides novel molecular markers and genomic resources to support phylogenetic reconstruction and species delimitation within the genus Lilium .