From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding

The genus <i>Cymbidium</i>, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among <i>Cymbidium</i> species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (<i>matK</i>, <i>rbcL</i>, <i>trnL-F</i>, <i>psbA-trnH</i>) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of <i>Cymbidium</i> species. The comparison of genetic distance variations showed that <i>psbA-trnH</i>, ITS + <i>psbA-trnH</i>, and ITS + <i>matK</i> + <i>psbA-trnH</i> exhibit minimal overlap and significant genetic variation within <i>Cymbidium</i> species. The phylogenetic analysis indicated that the combination, ITS + <i>matK</i> + <i>psbA-trnH</i>, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.