Abstract
Cathaya argyrophylla Chun et Kuang is a severely endangered, tertiary relict plant unique to China whose high physiological sensitivity to the environment, including photosensitivity, is likely closely related to its endangered status; however, the exact mechanism responsible has remained unknown due to the rarity of the plant and the difficulties involved in performing physiological studies on the molecular level. In this study, the chloroplast genomes of six C. argyrophylla populations sampled from different locations in China were characterized and compared. In addition, a gene regulatory network of the polymorphic chloroplast genes responsible for regulating genes found elsewhere in the plant genome was constructed. The result of the genome characterization and comparison showed that the genome characteristics, the gene composition, and the gene sequence of the chloroplast genes varied by location, and the gene regulatory network showed that the differences in growth location may have led to variations in the protein-coding chloroplast gene via various metabolic processes. These findings provide new insights into the relationship between chloroplasts and the sensitive metabolism of C. argyrophylla and provide additional reference materials for the conservation of this endangered plant.