Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

The genus has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various species, protection and sustainable development of rare resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for species. Here we determined the complete chloroplast (CP) genomes for , , , and through Illumina sequencing, followed by assembly. The lengths of the genomes ranged from 151,076 in to 152,043 in . Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. , , and equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas contained 132 unique genes due to absence of the gene. Subsequently, comparative analysis of the complete CP genomes revealed that , , , , - , - , , - , , and to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in and genera, a phylogenomic study was carried out with three species and five species as outgroups. The results of the phylogenetic analysis showed that was a sister to , and the interspecies relationships within subgenus were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.