The complete chloroplast genomes and phylogenetic analysis of <i>Lilium leichtlinii</i> var. <i>maximowiczii</i> from Northeast Asia

<i>Lilium leichtlinii</i> var. <i>maximowiczii</i>, native to Northeast Asia, shows morphological differences between Korean and Japanese varieties. This study analyzed chloroplast (cp) genomes of three diploid <i>L. leichtlinii</i> groups: Korean (KR), Japanese broad-leaved (JB), and Japanese narrow-leaved (JN). Genome sizes ranged from 152,053 bp to 152,588 bp with GC contents of 37.02-37.06%. All had typical quadripartite structures and contained 129 genes. Phylogenetic analysis of 48 <i>Lilium</i> cp genomes revealed at least three distinct <i>L. leichtlinii</i> varieties. Most genomic variation was found in non-coding regions, providing insights into intraspecific genomic diversity in <i>L. leichtlinii</i>.