title: 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.
authors.affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, No 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Chen
authors.forename: Jietang
authors.initials: J
authors.lastname: Zhao
authors.forename: David L
authors.initials: DL
authors.lastname: Erickson
authors.forename: Nianhe
authors.initials: N
authors.lastname: Xia
authors.forename: W John
authors.initials: WJ
authors.lastname: Kress
mesh_terms: D002681:China; D030024:Curcuma / Q000145:classification* / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D008969:Molecular Sequence Data; D002052:Myanmar; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer
keywords: DNA barcoding; ITS2; chloroplast region; species identification