Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matK.

Based on the morphological characteristics, botanists have so far identified 33 species belonging to 19 genera in 5 families of conifers in Vietnam. The largest family is the Pinaceae (5 genera, 12 species), followed by Cupressaceae (7 genera, 8 species), Podocarpaceae (4 genera, 6 species), Taxaceae (2 genera, 6 species), and Cephalotaxaceae (1 genus, 1 species). Of which, there are 29 species on the list of endangered species at the national level.

The Vietnamese conifer species are distributed in four main geographical regions, including the Northwest, Hoang Lien Son Mountain Range, limestone mountains in the North and the Northeast, and especially Central Highlands. Identifying conifer species is not an easy task in Vietnam. Traditional methods that are mainly based on phenotypic observations such as height, leaf shape and size, flower and fruit characteristics, etc., are not completely reliable as most of the parameters change normally by ages of plants, habitats, etc. Advanced methods are needed to support, accurately identify, and build phylogenetic relationships among conifers in Vietnam.

The study is a compilation of surveys, assessments, and collection of biological samples from 2009 to 2020 of the authors (under different research programs). We analyzed the nucleotide sequences of the two gene regions, rbcL and matK, in the chloroplast genome to identify the phylogenetic relationships among natural conifers in Vietnam and determine the most suitable DNA barcoding regions for those conifer species. This will form the basic foundation for conservation of genetic resources, evolutionary research, and biological systems of valuable conifers in the country.

Field survey at Pu Hoat Nature Reserve and Xuan Lien Nature Reserve

The findings of the study showed that the highest genetic distance was recorded between the species in Cupressaceae 5% (0.1-8.5), Podocarpaceae 6% (0-8.5), Taxaceae 5% (0.2-0.5), and Pinaceae 20.4% (0.8-54.1) in the matK region. In contrast, a low genetic distance between the species in Cupressaceae 2% (0-3.3), Podocarpaceae 3% (0.6-3.4), Taxaceae 1% (0-2.1), and Pinaceae 1.2% (0-5.82) was recorded in the rbcL region. The phylogenetic relationship between Vietnamese conifer species was reconstructed using two methods of Bayesian Inference (BI) and Maximum likelihood (ML) which indicated that the rbcL gene region was not detected between the species of Taxaceae and Cephalotaxaceae. However, the matK gene region was very clear in the different species among the families  of Cupressaceae, Podocarpaceae, and Cephalotaxaceae and unsuitable for identifying closely related species in Amentotaxus (Taxaceae) and Pinus (Pinaceae). The gene (matK) is a useful tool as a barcode in the identification of conifer species of Cupressaceae, Podocarpaceae, and Cephalotaxaceae in Vietnam.

 Phylogenetic relationships among Vietnamese conifer species based on the partial sequence of the chloroplast genes (matK) using the Maximum likelihood (ML)

 Phylogenetic relationships among Vietnamese conifer species based on the partial sequence of the chloroplast genes (rbcL) using the Maximum likelihood (ML)

Source: https://doi.org/10.17221/88/2020-CJGPB

Article and photos by: Pham Mai Phuong