Chloroplast genome comparison and chemical profiling support InDel based identification across cinnamon plants

Cinnamomum osmophloeum, an endemic edible species in Taiwan, is frequently misidentified as the invasive C. burmannii in commercial products. This study developed a DNA-based identification system using chloroplast insertion/deletion (indel) markers, supported by chemical profiling. The comparative analysis of chloroplast genomes between C. osmophloeum and other cinnamon species, yielding 15 indel loci, of which 14 were polymorphic and 6 revealed intraspecific variation. Eight validated indel markers were further used to discriminate cinnamon species. Volatile profiles analyzed by SPME-GC/MS showed that cinnamaldehyde and linalool dominated in C. osmophloeum, whereas borneol and eucalyptol characterized C. burmannii. Application to seven commercial products revealed that five products matched C. osmophloeum genotypes, consistent with labeling. These results demonstrate that chloroplast indel markers provide a robust and rapid tool for cinnamon authentication, while chemical profiling serves as a complementary approach for species discrimination.