Phylogenomics provides insights into the phylogeny of Liliales and the evolution of colchicine biosynthesis genes.

Liliales comprises many species of ecological, ornamental, and medicinal importance, yet its evolutionary relationships remain controversial. In particular, the origin and evolution of genes involved in colchicine biosynthesis are poorly understood. Here, we aimed to investigate phylogenetic uncertainties within Liliales and the evolution of colchicine-related genes. We sampled 203 transcriptomes (179 species), including 51 newly generated, representing eight families of Liliales. Then, we performed phylogenomic analyses including species tree inference, hybridization detection, and whole-genome duplication (WGD) assessment. We detected extensive phylogenetic conflict driven by incomplete lineage sorting and hybridization, and identified five WGD events across the order. Metabolite profiling confirmed colchicine in Colchicaceae species, and molecular analyses revealed that genes in its biosynthetic pathway are widely present in Liliales. Gene copy number, positive selection analyses, and molecular docking suggested that gene expansion and amino acid change (genes ABH1 and NAT1) contributed to colchicine biosynthesis. These findings indicate that WGDs and subsequent gene evolution contributed to the diversification of Liliales. This study provides new insights into the evolution of Liliales and the molecular basis of colchicine biosynthesis.