DNA Barcoding for Dipterocarpus Species in Vietnam Based on Chloroplast Gene Region matK

Abstract

Objective: Dipterocarp identification is challenging, based on traditional methods of morphological characteristics for species conservation and management. In the present study, the matK region was used as a DNA bar-code to identify the Dipterocarpaceae species in Vietnam. Methods: All the samples were collected at studied localities and identified by morphological methods by the botanist. DNA samples were extracted using the modified Cetyltrimethylammonium bromide method and amplified the matK gene by PCR. Sequencing was performed on an Avant 3100 Automated DNA sequencer system. Results: Thirty-three trees were analyzed, representing 11 species (eight in the Dipterocarpus genus, one in Hopea and one in Vativa) and showing low intraspecific divergence and interspecific divergence within and among Dipterocarpus species, with an average of 0.08% and 0.19%, respectively. However, there was zero distance between D. costatus, D. dyeri, D. intricatus and D. obtusifolius. Three Dipterocarpus species (D. alatus, D. condorensis and D. tuberculatus) were discriminated against, while others (D. costatus, D. dyeri and D. intricatus) showed too low divergent intraspecific lineages and suggested hybridization may be affected them. These results also indicated a low barcoding gap for Dipterocarpus species. The highest gene distance was found between Vatica and Dipterocarpus, with an average of 2.12%. Conclusion: In this study, we used the matK region as a tool to identify some Dipterocarpaceae species in Vietnam. The accurate identification of species may manage and conserve species effectively. Our results showed little sequence differentiation among most Dipterocarpus species. The lack of differentiation may be due to incomplete lineage sort and hybridization between sympatric species. In order to identify species, a combination of two or three chloroplast gene regions should be utilized in further studies. DNA barcoding gap should be analyzed within different genera in Dipterocarpaceae.