Comparative analysis of the complete chloroplast genome of seven Wikstroemia taxa (Thymelaeaceae) provides insights into the genome structure and phylogenetic relationships

New insights into the phylogeny of species in the family Thymelaeaceae and support of the recognition of D. genkwa and D. aurantiaca as species in the genus Wikstroemia are provided. Wikstroemia (Thymelaeaceae) is an economically important genus because some of its species are used in traditional medicine and also contribute to pulp production. The morphological characteristics of Wikstroemia species exhibit continuous natural variation, posing a challenge in accurately distinguishing this genus from its sister genera solely based on morphological traits. Consequently, the classification of, and phylogenetic relationships between, Wikstroemia and its sister genera, as inferred from morphological characteristics, remain contentious. Chloroplast genome information has proven to be a valuable tool in plant phylogeny. Here, we performed a comparative analysis of the chloroplast genomes of 15 species in the genus Wikstroemia, all of which exhibited typical quadripartite structures, with sizes ranging from 150,054 bp to 175,898bp. These genomes encoded 122–143 genes, including 79–95 protein-coding genes, 36–40 tRNA genes, and 8 rRNA genes. The overall GC content displayed minimal variation, ranging from 36.6% to 37.47%. The distributions of SSRs and codon bias exhibited similarities among Wikstroemia species. High variability hotspots were found in 15 intergenic spacers and 5 genes. Phylogenetic analyses consistently grouped all Wikstroemia species into a single clade. Notably, Daphne genkwa and D. aurantiaca were found to be nested within Wikstroemia, rather than being closely related to other Daphne species. Furthermore, phylogenetic analyses suggested that Wikstroemia is paraphyletic relative to Stellera chamaejasme. These findings provide new insights into the phylogeny of Wikstroemia and Daphne within the Thymelaeaceae, contributing to improved species identification and increasing the taxonomic and phylogenetic resolution of Wikstroemia.