Phylogeny and Comparative Analysis for the Plastid Genomes of Five (Liliaceae).

Species of (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of , but the molecular studies of species from this location are lacking. In our study, we assembled four plastid genomes from the Tien Shan Mountains, , , , and , combined with the plastid genome of to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five plastid genomes proved highly similar in overall size (151,691-152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of and the sister relationship between and , . , , and were clustered together, and was clustered with , with our results clearly demonstrating the relationships between these five species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of .