Complete chloroplast genome features and phylogenetic analysis of Clematis cadmia

Clematis cadmia (Ranunculaceae) is a herbaceous vine endemic to subtropical China. It is ecologically significant in riparian ecosystems along the Yangtze basin. C. cadmia also possesses horticultural appeal and is used in traditional medicine. This study presents the first assembly and annotation of the chloroplast genome of C. cadmia. High-throughput sequencing technology and bioinformatic analysis enabled this achievement. The chloroplast genome of C. cadmia exhibits a typical quadripartite structure and totals 159,672 bp. It consists of a large single-copy region (LSC), a small single-copy region (SSC), and inverted repeats (IRs). A total of 136 functional genes were annotated, including 36 tRNA genes, 8 rRNA genes, 91 protein-coding genes, and one pseudogene. Furthermore, 29 repeat structures and 241 SSR loci were identified. The genome displays an A/T-rich base composition and a clear A/U-ending codon preference. Comparative chloroplast genomic analyses revealed strong purifying selection during Clematis evolution and a highly conserved genomic architecture. Sliding window analysis identified four hypervariable regions as potential molecular markers. Phylogenetic reconstruction found that C. cadmia is most closely related to Clematis florida. The genus Clematis forms a strongly supported sister clade to Pulsatilla. This study provides fundamental data for molecular marker development, phylogenetic reconstruction, population genetics, and chloroplast genome engineering. These findings offer key insights into the resource utilization of C. cadmia.