Czech J. Genet. Plant Breed., 2021, 57(2):58-66 | DOI: 10.17221/88/2020-CJGPB

Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matKOriginal Paper

Mai Phuong Pham1, Viet Ha Tran2, Dinh Duy Vu*,1,3, Quoc Khanh Nguyen1, Syed Noor Muhammad Shah*,4
1 Vietnam-Russia Tropical Centre, Hanoi, Vietnam
2 College of Forestry, Vietnam National University of Forestry, Hanoi, Vietnam
3 Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
4 Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail Khan, Pakistan

We used two chloroplast gene regions (matK and rbcL) as a tool for the identification of 33 local conifer species. All 136 sequences, 101 newly generated (14 species for gene matK; 16 species for gene rbcL) and 35 retrieved from the GenBank, were used in the analysis. The highest genetic distance (matK region) was recorded between the species in Cupressaceae with an average of 5% (0.1-8.5), Podocarpaceae with an average of 6% (0-8.5), Taxaceae with an average of 5% (0.2-0.5) and Pinaceae with an average of 20.4% (0.8-54.1). The rbcL region showed 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). The phylogenetic analyses using the Maximum likelihood (ML) and Bayesian inference (BI) bootstrap values obtained at the branching nodes of each species ranged from 62 to 100% (Maximum likelihood bootstrap - MLBS and Bayesian posterior probabilities - BPP) for the matK gene; from 66 to 100% (MLBS) and 60 to 100% (BPP) for the rbcL region. The rbcL region was not identified between the species of Taxaceae and Cephalotaxaceae. The matK gene region was very clear in the different species among the families (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.

Keywords: DNA barcoding; endangered; phylogeny; taxonomy

Published: April 14, 2021  Show citation

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Pham MP, Tran VH, Vu DD, Nguyen QK, Shah SNM. Phylogenetics of native conifer species in Vietnam based on two chloroplast gene regions rbcL and matK. Czech J. Genet. Plant Breed. 2021;57(2):58-66. doi: 10.17221/88/2020-CJGPB.
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