Complete Chloroplast Genomes and Comparative Analyses of , , and (Amaryllidaceae).

The genus (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of , , and ; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven species were clustered into a monophyletic group, and closed to in Amaryllidaceae. , , and were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with . Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.