Abstract
Lilium cernuum is endangered and was listed in the category of key protected wild plants in China. In this study, we report the complete chloroplast genome of L. cernuum using Illumina paired-end sequencing. The entire chloroplast genome maps as a circular molecule of 152,604 bp built with a quadripartite organization: two inverted repeats (IRs) of 26,481 bp separated by a large single copy (LSC) sequence of 82,058 bp and a small single copy (SSC) sequence of 17,584 bp. The chloroplast genome contains the conservative structure present in most Liliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbor a single intron, and 2 contain a couple of introns. A maximum likelihood phylogenomic analysis showed that L. cernuum was closely related to L. tsingtauense and L. hansonii that belonged to the family Liliaceae.
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