Format: ORAL

Mingyue Ye1, Meizhen Wang1, Kenneth Cameron2, Pan Li1,*

1 Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China 2 Department of Botany, University of Wisconsin, Madison, USA * Corresponding author: panli@zju.edu.cn

The lily family (Liliaceae), which is distributed mainly across the temperate Northern Hemisphere, is of great horticultural, culinary, and medical importance. It is also a family with a long history of taxonomic uncertainty. Challenges in accurate species identification persist and phylogenetic relationships among genera within the family continue to be unresolved and/or weakly supported due to the use of limited molecular markers with insufficient variability. Here, plastome and transcriptome data were generated and combined with previously published data for this family, providing a total of 86 plastomes and 88 transcriptomes (plus one WGS data) covering all 15 currently recognized genera for analyses. Both plastid and nuclear phylogenomic analyses strongly confirm the recognition of four subfamilies: Tricyrtidoideae with four genera; Medeoloideae with two genera (Clintonia and Medeola); Lilioideae with eight genera; and a distinct subfamily, Calochortoideae, for Calochortus, which is sister to Medeoloideae and Lilioideae. Within Lilioideae, both plastid and nuclear phylogenomic analyses show that the Lilieae clade of (Notholirion, (Cardiocrinum, (Fritillatia, Lilium))) is sister to the Tulipeae clade of (Gagea, (Tulipa, (Erythronium, Amana))). However, plastid and nuclear trees show different topologies within Tricyrtidoideae, which is (Tricyrtis, (Streptopus, (Prosartes, Scoliopus))) in the plastid tree but (Tricyrtis, (Prosartes, (Streptopus, Scoliopus))) in the nuclear tree. This cytonuclear conflict is likely due to ancient hybridization. Our results provide a solid framework for future studies on the evolution of Liliaceae.