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

Abstract

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.

Phylogenetic Determination of Chenopodium quinoaBased on the Chloroplast Genes rbcL and matK

“…Te latter region evolves slowly and is, therefore, used more frequently in phylogenetic analyses [30]. In addition, the rbcL gene is a more universal region and is less efcient in separating closely related taxa [16], although some studies on angiosperm species have shown that this region presents enough variation to distinguish species [31]. Meanwhile, matK, which presents a faster evolution, is widely used for phylogenetic analyses.…”

“…Likewise, given the high conservation of its sequence, compact size, lack of recombination, and maternal inheritance, the chloroplast genome has been used for the generation of genetic markers and for phylogenetic classifcation [13], genetic divergence [14], and DNA barcoding systems for molecular identifcation [15]. Commonly studied chloroplast coding genes include atpF-atpH, matK, rbcL, rpoB, rpoC1, psbK-psbL, and trnH-psbA since they meet the requirements for use as DNA barcodes in plants [16]. Hollingworth et al (2009) recommended the combination of two loci, ribulose-1,5-bisphosphate carboxylase (rbcL) and maturase (matK), as a plant barcode based on assessments of recoverability, sequence quality, and levels [17].…”

Identification of Egyptian Mangrove Species Based on DNA Barcoding

“…For greater plant group resolution, it is interesting to note that numerous scientists have suggested merging different barcoding sites or entire chloroplast genome sequences [48,49]. Several authors have demonstrated the utility of single barcoding loci to differentiate between plant species, including conifers [50] and bamboo [51], wild cherry [52], and zingiber [53]. The results showed that each individual and combination of loci raised the level of discrimination between selected mangrove species.…”

Genetic structure in natural populations of Dacrydium elatum (Roxb.) Wall. (Podocarpaceae) in the Central Highlands of Vietnam inferred by Microsatellites

“…Wall. genus Dacrydium (Podocarpaceae) isconifer species in Vietnam, grows in primary closed evergreen seasonal forest tropical mixed (elevations 700-2000m) they have been extensively used for furniture, handicrafts and construction [1][2][3]. In Vietnam it is found in Ha Giang, Tuyen Quang, Quang Ninh, Lai Chau, Ha Tinh, Quang Binh, Thua Thien Hue, Da Nang, Kon Tum, Gia Lai, Dak Lak, Lam Dong and Kien Giang provinces and other countries like China, Laos, Cambodia, Thailand, Malaysia and Indonesia [1][2].…”