Complete chloroplast genomes of the hemiparasitic genus : Insights into comparative analysis, development of molecular markers, and phylogenetic relationships.

The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus has yet to be reported. In addition, the traditional Mongolian medicine is frequently subjected to adulteration or substitution because of the minor morphological differences with . In this study, the complete chloroplast genomes of the two species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes () and a unique L-K inversion. Unlike the high variability observed in holoparasites, and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus and the - clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "".