Comparative Analysis of Complete Chloroplast Genomes and Multiple DNA Sequences Reveals Interspecific Relationships of C. bretschneideri and Related Species in China

Crataegus L. is a genus in the family Rosaceae with medicinal properties and health benefits. The taxonomic and phylogenetic relationships of C. bretschneideri have been of interest due to lack of effective markers. We assembled the chloroplast genomes of C. bretschneideri and related four species. The length of chloroplast genomes were ranging from 159,644 bp (C. bretschneideri) to 159,947 bp (C. pinnatifida var. major). Five chloroplast genomes had similar feature and possessed from 86 to 88 protein coding genes, 37 tRNA genes and 8 rRNA genes arranged in the same order. Eight hotspot regions including ndhJ, atpA, trnQ-UUG-psbK and ycf1 were identified that could be used as potential molecular markers. We also proposed divergence times for C. bretschneideri based on chloroplast genome. Phylogenetic analyses, supported by chloroplast genome and nuclear sequencing, indicated that C. bretschneideri might arose through hybridization between C. pinnatifida and C. maximowiczii. It provides a new insight into the hybrid origin of C. bretschneideri resources.