Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny.

(Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of , but also among species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of chloroplast genomes. Furthermore, four mutational hotspots (, , , and ) with π > 0.004 were identified as potential molecular markers for species. Phylogenomic analysis strongly supported that the red flower phenotype of was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of species but also could be used as potential genetic resources for Chinese firethorn breeding.