Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China

Abstract

The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers.

Genetic mutation in mangroveAcanthus ilifoliciusbase on DNA Barcode (rbcL and matK gen) in the different environment change in coastal Cilacap, Central Java, Indonesia

“…The species discrimination was lower (<50 %) for rbcL + matK combination in the study of tropical tree species in French Guiana [13]. Lower discriminationwere reported in closest and complex taxa of Lysimachia, Ficus, Holcoglossum and Curcuma using rbcLand matK [39], [41], [22], [5]. The lowest discriminatory power was observed in closely related groups of Lysimachia with rbcL (26.5-38.1 %), followed by matK (55.9-60.8 %) and combinations of core barcodes (rbcL + matK) had discriminationof 47.1-60.8 % [41].…”

“…The amplified products were separatedby agarose gel (1.2 %) electrophoresis and stainedwith ethidium bromide [35]. Two pair of universal primers rbcL (rbcLa_F and rbcLa_R) and matK_390f and matK_1326r were used for the amplification purpose [19], [5]. PCR amplification was performed using forward and reverse primers [3].…”

Assessment of Genetic and Chemical Variability in Curcumae Longae Rhizoma (<i>Curcuma longa</i>) Based on DNA Barcoding Markers and HPLC Fingerprints

“…9,12) Using clone sequencing for ITS-LSU D1/D3, we identified 2-10 haplotypes within each sample. Our results are consistent with other studies 10,11) reported different ITS sequences among specimens.…”

“…Previous studies tested the ability of DNA barcoding to identify Curcuma species. [9][10][11][12] This research yielded sequence data that are stored in GenBank and can be used as a reference library. To improve the efficiency of rbcL and matK, we used the nuclear ribosome fragment ITS-LSU D1/D3 (Fig.…”

The phylogenetic analysis of Dalbergia (Fabaceae: Papilionaceae) based on different DNA barcodes

“…Furthermore, the region of nuclear ribosomal internal transcribed spacer (ITS) and the ITS2 region were also suggested as an alternative source of barcoding for flora (Chen et al 2010a;China Plant BOL Group 2011). Single or combined barcodes allows the identification of different species for a number of genera (Ibeiro et al 2007;Gonzalez et al 2009;Chen et al 2014;Jiao et al 2014). Hassold et al (2016) demonstrated that DNA barcoding is efficient to discriminate between Malagasy and non-Malagasy Dalbergia species.…”