Analysis of chloroplast genomes of ten central Asian Fritillaria species and their phylogenetic relationships

Fritillaria is a taxonomically complex genus of Liliaceae that contains many important ornamental and medicinal species. In this study, we sequenced the chloroplast genomes of ten Fritillaria species distributed in central Asia and compared them to previously sequenced Fritillaria cp genomes. Comparison of 36 Fritillaria species' cp genomes identified as useful potential molecular markers due to their high level of divergence three coding regions and 11 intergenic spacers. Effective single sequence repeats (SSRs) for population genetic studies of Fritillaria were also identified. Phylogenetic analysis showed that two recently described species, F. baisunensis and F. rugillosa belong to F. subg. Rhinopetalum, and that the belonging of F. ussuriensis and F. meleagroides in F. subg. Fritillaria should be revised. These two species and F. camschatsencese currently assigned to F. subg. Liliorhiza, should be members of the same taxonomic unit. Fritillaria subg. Liliorhiza, although a small group, is more complicated than it was previously thought, and apparently comprises species too distant to be in one subgenus. Fritillaria maximowischii, currently assigned to F. subg. Liliorhiza should be treated as a new subgenus.