The Chloroplast Genome of Lilium henrici: Genome Structure and Comparative Analysis

Abstract

<i>Lilium henrici</i> Franchet, which belongs to the family Liliaceae, is an endangered plant native to China. The wild populations of <i>L. henrici</i> have been largely reduced by habitat degradation or loss. In our study, we determined the whole chloroplast genome sequence for <i>L. henrici</i> and compared its structure with other <i>Lilium</i> (including <i>Nomocharis</i>) species. The chloroplast genome of <i>L. henrici</i> 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 <i>L. henrici</i> 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 <i>L. henrici</i> chloroplast genome sequence. Genic comparison among <i>L. henrici</i> with other <i>Lilium</i> (including <i>Nomocharis</i>) chloroplast genomes shows that the sequence lengths and gene contents show little variation, the only differences being in three pseudogenes. Phylogenetic analysis revealed that <i>N. pardanthina</i> was a sister species to <i>L. henrici</i>. Overall, this study, providing <i>L. henrici</i> genomic resources and the comparative analysis of <i>Lilium</i> chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus <i>Lilium</i>, molecular barcoding in population genetics.