Stachyurus , the sole genus of the Stachyuraceae family, comprises approximately 10 species distributed across eastern Asia, with potential applications in horticulture and medicine. However, limited genetic resources have hindered comprehensive research on this genus. Here, we sequenced and assembled the complete chloroplast genomes (cpDNAs) of 25 Stachyurus accessions, representing seven currently accepted species and one variety. The assembled Stachyurus cpDNAs range from 161,624 to 162,947 bp in length, with a GC content of 37.0–37.1% and 129–131 genes. Comparative analyses revealed a high degree of conservation in genome size, structure, inverted repeat (IR) boundary dynamics, GC content, and repeat patterns. Nevertheless, subtle variations driven by IR boundary shifts, gene loss (particularly ycf15 ), and differences in long sequence repeats collectively account for the observed cpDNA length variation. Seven hypervariable regions as promising molecular markers and four genes exhibited signatures of positive selection were identified. Phylogenetic analyses based on complete cpDNAs showed widespread paraphyly and strong cytonuclear discordance with previous nuclear phylogenies, providing clear evidence of chloroplast capture associated with hybridization. While reciprocal monophyly between Chinese and Japanese species was supported, relationships within the Chinese clade remain poorly resolved. These findings underscore the limitations of plastid data alone and highlight the urgent need for integrative studies combining nuclear genomic data, dense population sampling, and morphological/ecological information to clarify species boundaries and taxonomic relationships within Stachyurus . This study provides essential chloroplast genomic resources for future phylogenetic, phylogeographic, and adaptive evolution research on this understudied genus.
Liu et al. (2026) studied this question.