Genetic evaluation and classification of hard-leaf <i>Cymbidium </i> orchids based on DNA barcoding markers

Truong Giang Nguyen; Phuong Thao Pham; Van Biet Huynh; Huu Duc Huynh

doi:10.15625/vjbt-23173

Author affiliations

Authors

Truong Giang Nguyen \(^1\) Biotechnology Center of Ho Chi Minh City, 2374 Do Muoi, Quarter 10, Trung My Tay, Ho Chi Minh City, Vietnam
\(^2\) Faculty of Biological Sciences, Nong Lam University – Ho Chi Minh City, Quarter 33, Linh Xuan, Ho Chi Minh City, Vietnam https://orcid.org/0000-0002-1716-0874
Phuong Thao Pham \(^1\) Biotechnology Center of Ho Chi Minh City, 2374 Do Muoi, Quarter 10, Trung My Tay, Ho Chi Minh City, Vietnam
Van Biet Huynh \(^3\) Research institute for Biotechnology and Environment, Nong Lam University – Ho Chi Minh City, Quarter 33, Linh Xuan, Ho Chi Minh City, Vietnam https://orcid.org/0000-0001-7154-8776
Huu Duc Huynh \(^1\) Biotechnology Center of Ho Chi Minh City, 2374 Do Muoi, Quarter 10, Trung My Tay, Ho Chi Minh City, Vietnam https://orcid.org/0009-0002-0450-7645

DOI:

https://doi.org/10.15625/vjbt-23173

Keywords:

Cymbidium, DNA barcoding markers, genetic diversity, genetic resources, maturase K (matK), sequencing.

Abstract

The hard-leaf Cymbidium orchid group comprises several species within the genus Cymbidium, including Cymbidium finlaysonianum, Cymbidium aloifolium, Cymbidium bicolor, and Cymbidium atropurpureum, which are adapted to tropical and subtropical climates. These native Vietnamese orchids have high economic value and are currently overexploited in the wild. To conserve and utilize these genetic resources, 19 samples of hard-leaf Cymbidium orchids from various regions were analyzed and genetically evaluated using DNA barcoding markers. The analysis of two chloroplast gene regions (rbcL and matK) and one nuclear gene region (ITS2) revealed the sizes of each gene region: rbcL (680-715 bp), matK (760-762 bp), and ITS2 (453 bp). Comparing the DNA sequences of these regions among the samples showed both conservation and diversity within and between species, with conserved sites (678/715, 744/762, 228/453), variable sites (37/715, 18/762, 225/453), Pi (36/715, 11/762, 191/453), and InDels (35/715, 2/762, 0/453). Phylogenetic analysis indicated that the matK gene could clearly distinguish four species; however, the rbcL gene could not differentiate between C. aloifolium and C. atropurpureum. The ITS2 region displayed high intraspecific variation but was insufficient for species discrimination. Combining rbcL and matK regions provided both intra-species diversity insights and effective species discrimination. These findings demonstrate that DNA barcoding markers are useful for species identification and assessing genetic diversity among the four hard-leaf Cymbidium orchids. They also highlight some limitations of using the ITS2 region for species identification in some instances.

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