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Franchet, which belongs to the family Liliaceae, is an endangered plant native to China. The wild populations of
have been largely reduced by habitat degradation or loss. In our study, we determined the whole chloroplast genome sequence for
and compared its structure with other
(including
) species. The chloroplast genome of
is a circular structure and 152,784 bp in length. The large single copy and small single copy is 82,429 bp and 17,533 bp in size, respectively, and the inverted repeats are 26,411 bp in size. The
chloroplast genome contains 116 different genes, including 78 protein coding genes, 30 tRNA genes, 4 rRNA genes, and 4 pseudogenes. There were 51 SSRs detected in the
chloroplast genome sequence. Genic comparison among
with other
(including
) chloroplast genomes shows that the sequence lengths and gene contents show little variation, the only differences being in three pseudogenes. Phylogenetic analysis revealed that
was a sister species to
. Overall, this study, providing
genomic resources and the comparative analysis of
chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus
, molecular barcoding in population genetics.