The complete plastome sequence of Lilium primulinum var. burmanicum, an ornamental and medicinal plant endemic to China

Lilium primulinum var. burmanicum (W. W. Smith) Stearn 1948 is an ornamental and medicinal plant that has an extremely limited distribution in Yunnan, China. Here, we obtained the complete plastome of L. primulinum var. burmanicum via next-generation sequencing, and conducted phylogenomic analyses with existing species from Lilium. The total length of L. primulinum var. burmanicum was 152,206 bp with a typical quadripartite structure. The whole plastome contained a pair of inverted repeats (IRa/IRb; 26,399 bp) which divided a large single-copy (LSC; 81,854 bp) and a small single-copy (SSC; 17,563 bp). The average GC content among the whole plastome sequence and the LSC, SSC, and IR regions were 37%, 34.8%, 30.6%, and 42.5%, respectively. There were 134 genes detected from the whole plastome sequence, including 87 protein-coding genes, 39 tRNAs, and 8 rRNAs. Phylogenetic analyses using maximum likelihood showed congruent results that L. primulinum var. burmanicum together with L. primulinum var. ochraceum formed a single branch. These results demonstrate a close relationship between these variation species. The newly characterized chloroplast genome presented here will provide essential data for further phylogenomic analyses of the intraspecific relationship among Lilium species and for conservation genetics research of L. primulinum var. burmanicum.